AMENDED AND RESTATED COLLABORATIVE RESEARCH AGREEMENT

EXHIBIT 10.3A

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

AMENDED AND RESTATED COLLABORATIVE RESEARCH AGREEMENT

THIS AMENDED AND RESTATED COLLABORATIVE RESEARCH AGREEMENT, together with exhibits and schedules attached hereto, (the “Amended and Restated Research Agreement” or the “Agreement”) is entered into as of the Execution Date and effective as of November 1, 2006 (the “Effective Date”), by and between Equilon Enterprises LLC dba Shell Oil Products US, a Delaware limited liability company, having a place of business at 000 Xxxxxxxxx Xxxxxx, Xxxxxxx, Xxxxx 00000 (“Shell”), and Codexis, Inc., a Delaware corporation, having a place of business at 000 Xxxxxxxxx Xxxxx, Xxxxxxx Xxxx, Xxxxxxxxxx 00000 (“Codexis”). Shell and Codexis may each be referred to herein individually as a “Party” or, collectively, as the “Parties.”

RECITALS

WHEREAS, Codexis possesses certain valuable business and/or technical knowledge, information and/or expertise applicable to the enhancement of the performance of certain enzymatically catalyzed processes.

WHEREAS, Shell and Codexis entered into a certain Collaborative Research Agreement, effective as of November 1, 2006, as amended, pursuant to which Codexis has agreed to work exclusively with Shell in the Field of Use (as defined below) to develop certain new biocatalytic processes for use in the conversion of biomass to fuels and/or fuel additives and/or lubricants.

WHEREAS, the Parties desire to amend and restate such Collaborative Research Agreement to revise the scope of, and increase the resources devoted to, the collaboration between the Parties, all on the terms and conditions set forth below.

NOW, THEREFORE, in consideration of the promises and undertakings set forth herein, the Parties agree as follows:

ARTICLE 1

DEFINITIONS

Capitalized terms not otherwise defined herein will have the meaning set forth below:

1.1 “Acquired Technology” has the meaning set forth in Section 7.1.

1.2 “Affiliate” means,

(a) with respect to Codexis, any business entity controlling, controlled by, or under common control with Codexis. For the purpose of this Section 1.2(a) only, “control” means (i) the possession, directly or indirectly, of the power to direct the management or policies of a business entity, whether through the ownership of voting securities, by contract or otherwise, or (ii) the ownership, directly or indirectly, of at least fifty percent (50%) of the voting securities

or other ownership interest of a business entity; provided that, if local law requires a minimum percentage of local ownership, control will be established by direct or indirect beneficial ownership of one hundred percent (100%) of the maximum ownership percentage that may, under such local law, be owned by foreign interests; and

(b) with respect to Shell, Royal Dutch Shell plc and any company (other than Shell) which is from time to time directly or indirectly affiliated with Royal Dutch Shell plc. For the purpose of this Section 1.2(b) only, a particular company is (i) directly affiliated with another company or companies if that latter company beneficially owns or those latter companies together beneficially own fifty per cent or more of the voting rights attached to the ownership interest of the particular company; and (ii) is indirectly affiliated with company or companies if a series of companies can be specified, beginning with that latter company or companies and ending with the first mentioned company, so related that each company of the series (except the latter company or companies) is directly affiliated with one or more of the companies earlier in the series.

1.3 “Amended and Restated License Agreement” means the Amended and Restated License Agreement entered into by Shell and Codexis on the Execution Date and effective as of the Effective Date.

1.4 “Biocatalyst” means an enzyme or a Microbe that can enzymatically catalyze a particular chemical reaction, and which enzyme or Microbe arose out of the Program.

1.5 “Biomass” means organic, non-fossil, plant-derived matter available on a renewable basis, including, for example, crops and/or trees grown or harvested for use for fuel and/or fuel additive production, agricultural food and feed crops, aquatic plants and, in each case, organic wastes derived from the foregoing, including municipal wastes (e.g., newspapers).

1.6 “Codexis Technology” means (a) the Shuffling Technology and any improvements to the Shuffling Technology developed by employees of or consultants to Shell and/or employees of or consultants to Codexis in performance of the Program; and (b) any other Technology that is or was (i) developed by employees of or consultants to Codexis, alone or jointly with Third Parties, prior to or during the Term outside the scope of activities described in any Research Plan; or (ii) acquired during the Term by purchase, license, assignment or other means from Third Parties by Codexis, in each of case (b)(i) and (b)(ii), introduced by Codexis into the activities to be conducted under any Research Plan.

1.7 “Confidential Information” means any and all non-public and proprietary Information that is specifically designated as such and that is disclosed by either Party to the other in written or other similar form in connection with this Amended and Restated Research Agreement and that, if orally or visually disclosed, shall be summarized in writing in detail and specifically designated as proprietary and such summary delivered to the receiving Party within thirty (30) days after such disclosure.

1.8 “Contract Year” means a year beginning on the Effective Date, or an anniversary of the Effective Date during the Term, and ending one (1) year after such respective date.

1.9 “Control” means, with respect to an item, Information, Patent Right or an intellectual property right, possession of the ability, whether arising by ownership or license or otherwise, to grant a license or sublicense as provided for herein under such item, Information, Patent Right or right without violating the terms of any written agreement with a Third Party.

1.10 “Execution Date” means November 1, 2007.

1.11 “Field of Use” means the conversion of (a) Biomass into fermentable sugars, such sugars to be converted into (i) liquid fuel and/or liquid fuel additives and/or (ii) Lubricants, and (b) fermentable sugars derived from Biomass into (i) liquid fuel and/or liquid fuel additives, and/or (ii) Lubricants. For purposes of this Section 1.11 only, (1) “liquid” means a substance that is a liquid at a temperature of twenty-five (25) degrees Celsius under atmospheric pressure, and (2) “fuel additive” means a substance which is added to fuel to modify the characteristics of such fuel, including, for example, biodegradability, combustibility, viscosity, performance and/or emissions profile. For avoidance of doubt the “Field of Use” shall not include any material obtained from Biomass that is used as an ingredient in human food or animal feed products.

1.12 “FTE” means the efforts of one or more employees of Codexis equivalent to the efforts of one Codexis full time employee (i.e., an employee that works at least one thousand seven hundred sixty (1760) hours per year).

1.13 “Information” means data, results, evaluations, inventories, Microbes, show-how, know-how, computer chip and programs, processes, machines, biological chemicals, intermediates, trade secrets, techniques, methods, developments, materials, methods of analysis, compositions of matter, copyrights or other information.

1.14 “Lubricant” means materials compounded or blended from ingredients that are used primarily for lubrication of motor vehicles or mobile or stationary machinery or equipment, including engine oils, power steering fluids, transmission fluids, brake fluids, gear oils, shock absorber fluids, industrial fluids, process oils, metalworking oils, cutting oils, electrical oils, hydraulic oils, railroad oils, refrigerator oils, aircraft turbine, aircraft hydraulic and aircraft engine oils, food grade oils, turbine oils, greases and by-products of compound blending such as line wash, line clippings, cut oil and off-specification grease.

1.15 “Microbes” means whole (live or dead) prokaryotic organisms and/or yeasts and/or fungi or extracts thereof. Microbes shall not include land plants, including nonseed plants (Bryophytes, Tracheophytes) such as liverworts, mosses, ferns, and seed plants, such as gymnosperms and angiosperms (monocot and dicots); and/or non-land plants, including Prasinophytes, Chlorophyceae, Trebouxiouphyceae, Ulvophyceae, Chlorokybales, Streptophyta, Klebsormidiales, Zygnematales, Charales, Coleochaetales and Embryophytes.

1.16 “Oversight Committee” has the meaning set forth in Section 2.3(a).

1.17 “Patent Rights” means all patent applications and patents, whether domestic or foreign, covering patentable inventions within the Codexis Technology, the Shell Technology and the Program Technology, as applicable, all continuations, continuations-in-part and divisions of such patent applications and of patent applications from which such patents issued, all patents

issuing from any of such patent applications, and all renewals, reissues, re-examinations and extensions of any of such patents.

1.18 “Program” means the program of activities conducted by Codexis and/or Shell pursuant to this Amended and Restated Research Agreement, as further described in the Research Plans.

1.19 “Program Technology” means Technology (other than Codexis Technology and/or Shell Technology) either (a) developed by employees of or consultants to Shell and/or employees of or consultants to Codexis during the Term in the course of activities described in the Research Plans; or (b) acquired during the Term by purchase, license, assignment or other means from Third Parties by Codexis and/or Shell for the purpose of the Research Plans.

1.20 “Research Committee” has the meaning set forth in Section 2.2(a).

1.21 “Research Plan” means a written plan to be agreed upon by the Parties describing activities to be carried out in connection with each work stream, which plan may be amended from time to time by agreement between the Parties. Each Research Plan, and any amendment thereto, shall be attached to this Amended and Restated Research Agreement as a schedule to Exhibit 1.21.

1.22 “Series D Stock Purchase Agreement” has the meaning set forth in Section 3.5(a).

1.23 “Series E Stock Purchase Agreement” has the meaning set forth in Section 3.5(b).

1.24 “Shell Technology” means any Technology that is or was (a) developed by employees of or consultants to Shell or an Affiliate of Shell, alone or jointly with Third Parties, prior to or during the Term outside the scope of activities described in any Research Plan; or (b) acquired during the Term by purchase, license, assignment or other means from Third Parties by Shell or an Affiliate of Shell, in each of case (a) or (b), introduced by Shell into the activities to be conducted under any Research Plan.

1.25 “Shuffling” means the characterization, development and optimization of genes and proteins for commercial uses through the recombination and/or rearrangement and/or mutation of genetic material for the creation of genetic diversity.

1.26 “Shuffling Technology” means any and all techniques, methodologies, processes, materials and/or instrumentation Controlled by Codexis, including without limitation any and all patent rights, know-how, confidential information and materials relating thereto, that, in each case, relates to Shuffling, and generally applicable screening techniques, methodologies, or processes of using the resulting genetic material to identify potential usefulness.

1.27 “Technology” means and includes all materials, technology, technical information, intellectual property, know-how, expertise and trade secrets related to the Field of Use.

1.28 “Term” has the meaning set forth in Section 11.1.

1.29 “Third Party” means any party other than Codexis, Shell or Affiliates of either Party.

1.30 “Warrant Agreement” has the meaning set forth in Section 8.2.

1.31 “Year Four Goal(s)” shall have the meaning set forth in Section 2.8(c).

1.32 “Year One Final Milestone” shall mean the achievement of the criteria set forth on Exhibit 1.32.

1.33 “Year Six Goal(s)” shall have the meaning set forth in Section 2.8(d).

ARTICLE 2

PROGRAM ACTIVITIES

2.1 Purpose. Codexis and Shell shall conduct the Program during the Term. The objective of the Program is to utilize Shuffling Technology to conduct research, and to discover and develop Biocatalysts, and associated processes for the use of such Biocatalysts, in the Field of Use, all as described in further detail in the Research Plans.

2.2 Research Committee.

(a) Function. Shell and Codexis shall establish a Research Committee (the “Research Committee”) to:

(i) review the Research Plans as proposed by the Parties pursuant to Section 2.7, and to make recommendations to the Oversight Committee with respect to such proposed Research Plans;

(ii) review and evaluate progress under the Research Plans;

(iii) amend the Research Plans, as appropriate;

(iv) review annual milestones for activities to be carried out under each Research Plan by the Parties as defined and pursuant to Section 2.8(b), and to make recommendations to the Oversight Committee with respect to such proposed Milestones;

(v) review the Year Four Goal(s) proposed by the Parties pursuant to Section 2.8(c), and to make recommendations to the Oversight Committee with respect to such proposed Year Four Goal(s) on or before the May 1, 2009;

(vi) review the Year Six Goal(s) proposed by the Parties pursuant to Section 2.8(d), and to make recommendations to the Oversight Committee with respect to such proposed Year Six Goal(s) on or before May 1, 2010;

(vii) make recommendations to the Oversight Committee with respect to whether Milestones for the activities to be carried out under each Research Plan, the Year Four Goal(s) and the Year Six Goal(s) have been achieved;

(viii) coordinate and monitor publication of research results obtained from, and the exchange of Information that relates to, the Program;

(ix) review and, if appropriate, investigate through appointment of a patent subcommittee or otherwise, at the election of the Research Committee, any issues that either Party may raise with respect to intellectual property rights of any Third Party directly relevant to the activities under the Research Plans and to make recommendations to the Parties regarding the appropriate action, if any, with respect thereto, including, for example, a recommendation to obtain a license from a Third Party. For purposes of clarification, each Party shall notify the other Party, through the Research Committee, of any and all intellectual property of a Third Party which the notifying Party believes is directly relevant to the activities under the Research Plans which such Party becomes aware during the Term; and

(x) provide a written meeting discussion summary to the Oversight Committee of each meeting of the Research Committee within ten (10) business days after each such meeting.

(b) Membership. Shell and Codexis each, in its sole discretion, shall appoint three (3) members to the Research Committee and shall provide written notice to the other Party of the names and contact information of such three (3) members within five (5) days after the Effective Date. Each Party may appoint substitutes for its members at any time, such substitution to be effective immediately upon providing the name and contact information of such substitute to the other Party’s representatives on the Research Committee.

(c) Chair. The Research Committee shall be chaired by two (2) co-chairpersons, one appointed by Shell and one appointed by Codexis.

(d) Meetings. The Research Committee shall meet at least quarterly, at places and on dates selected in turn by each Party. Representatives of Shell or Codexis or both, in addition to members of the Research Committee, may attend such meetings at the invitation of either Party.

(e) Minutes. The Research Committee shall keep accurate written minutes of its deliberations that record all proposed decisions and all actions recommended or taken. Drafts of the minutes shall be delivered to all Research Committee members within ten (10) business days after each such meeting. The Party hosting the meeting shall be responsible for the preparation and circulation of the draft minutes. Draft minutes shall be edited within ten (10) business days after reception of the draft minutes by the co-chairpersons and shall be issued in final form only after each chairperson provides their respective approval and agreement. A final copy of the minutes shall be issued no later than thirty (30) business days after each respective meeting.

(f) Decisions.

(i) Decision Making Process of the Research Committee. All decisions of the Research Committee shall be made by unanimous vote or written consent, as indicated by both co-chairpersons of the Research Committee signing the final written minutes thereof. Codexis representatives collectively shall have one (1) vote and Shell representatives collectively shall have one (1) vote; provided, however, that in the case of a deadlock where unanimity has not been reached, the final decision with respect to matters concerning technical aspects within the scope of an approved Research Plan shall be made by Codexis; provided further, that the scope and goal(s) of such Research Plan, including (A) the annual Milestone(s) for such Research Plan, the Year Four Goal and the Year Six Goal, and (B) whether such Milestone(s), Year Four Goal and Year Six Goal have been achieved, shall never be considered “technical aspects.” If a disagreement among members of the Research Committee with respect to matters other than “technical aspects” remains unresolved for more than thirty (30) business days after the Research Committee first addresses such matter (or such longer period as the Parties may mutually agree upon), such disagreement shall be submitted to the Oversight Committee for resolution. Notwithstanding anything to the contrary, the Research Committee shall have no authority to alter, modify or amend any of the rights and obligations of the Parties set forth under this Amended and Restated Research Agreement.

(ii) Decision Making Process if the Research Committee is Disbanded. If the Research Committee is disbanded pursuant to Section 2.2(h), then after such disbanding, decisions formerly within the jurisdiction of the Research Committee shall be submitted to the Oversight Committee for resolution. If the Oversight Committee has been disbanded pursuant to Section 2.3(h), then decisions shall be submitted to senior executive officers of each Party having authority to make decisions in such matters as designated by each Party in a written notice to the other Party (“Executives”), subject to the decision making processes and principles set forth in Section 2.3(f)(i) as if Section 2.3(f)(i) applied to decisions to be made by such Executives.

(g) Expenses. Shell and Codexis shall each bear all expenses of their respective members related to their participation on the Research Committee.

(h) Disbanding of the Research Committee. The Parties shall have the right to disband the Research Committee upon mutual agreement. Failure to agree to disband the Research Committee shall not constitute a breach of this Agreement, nor trigger the Dispute Resolution process as described in Section 12.7. The Research Committee shall be automatically disbanded upon the expiration or termination of the Agreement as set forth in Article 11.

2.3 Oversight Committee.

(a) Function. Shell and Codexis shall establish an Oversight Committee (the “Oversight Committee”) to:

(i) set priorities for the Parties’ performance under the Program;

(ii) review summaries of meetings and other reports of the Research Committee;

(iii) review and approve recommendations from the Research Committee with respect to the Milestones for the activities to be carried out for each Research Plan, the Year Four Goal(s) and the Year Six Goal(s), and to approve such Milestones;

(iv) determine whether Milestones for the activities to be carried out under each Research Plan, the Year Four Goal(s) and the Year Six Goal(s) have been achieved;

(v) review, provide comment on, and approve Research Plans;

(vi) review the activities and obligations of the Parties and the Research Committee under this Agreement;

(vii) resolve any disputes or disagreements submitted to it by the Research Committee, and, if applicable, submit disputes or disagreements that it does not resolve within the time provided in Section 2.3(f)(i) to designated Executives of the Parties, as further described in Section 2.3(f)(i);

(viii) review all material data arising in the course of activities conducted pursuant to this Amended and Restated Research Agreement by either Party;

(ix) appoint subcommittees as it deems appropriate for carrying out the Program; and

(x) perform such other functions as appropriate to further the purposes of this Amended and Restated Research Agreement as determined by the Parties, including without limitation the periodic evaluation of performance against goals.

(b) Membership. Shell and Codexis each, in its sole discretion, shall appoint three (3) members to the Oversight Committee and shall provide written notice to the other Party of the names and contact information of all such members within five (5) days after the Execution Date. Each Party may appoint substitutes for its members at any time, such substitution to be effective immediately upon providing the name and contact information of such substitute to the other Party’s representatives on the Oversight Committee.

(c) Chair. The Oversight Committee shall be chaired by two (2) co-chairpersons, one appointed by Shell and one appointed by Codexis.

(d) Meetings. The Oversight Committee shall meet at least bi-annually, at places and on dates selected in turn by each Party. Representatives of Shell or Codexis or both, in addition to members of the Oversight Committee, may attend such meetings at the invitation of either Party.

(e) Minutes. The Oversight Committee shall keep accurate written minutes of its deliberations that record all proposed decisions and all actions recommended or taken. Drafts

of the minutes shall be delivered to all Oversight Committee members within ten (10) business days after each meeting. The Party hosting the meeting shall be responsible for the preparation and circulation of the draft minutes. Draft minutes shall be edited by the co-chairpersons and shall be issued in final form only after each chairperson provides their respective approval and agreement. A final copy of the minutes shall be issued within thirty (30) business days after each respective meeting.

(f) Decisions.

(i) Decision Making Process of the Oversight Committee. All decisions of the Oversight Committee shall be made by unanimous vote or written consent, as indicated by the co-chairpersons of the Oversight Committee signing the written minutes thereof, with Codexis representatives collectively having one (1) vote and Shell representatives collectively having one (1) vote; provided, however, that in the case of a deadlock where unanimity has not been reached, the final decisions shall be made by Shell except with respect to (A) the approval or modification of the annual Milestone(s) for each Research Plan, the Year Four Goal(s) or the Year Six Goal(s), (B) the approval or amendment of any Research Plan, (C) the determination as to whether Milestones for the activities to be carried out under each Research Plan, the Year Four Goal(s) or the Year Six Goal(s) have been achieved, (D) the acquisition of Third Party rights pursuant to Section 7.1, (E) the determination to have any party that is a Third Party as of the Execution Date participate in the activities to be conducted under the Program, (F) the introduction of Third Party Information into the Program, or (G) any decision that has a reasonable likelihood of having a material adverse impact on Codexis’ business as conducted at the time of such decision or as contemplated to be conducted at the time of such decision. Notwithstanding anything to the contrary, except with respect to the approval of the Research Plans, the annual milestones for the activities carried out under each Research Plan, the Year Four Goal(s), the Year Six Goal(s), and any amendments to any of the foregoing, the Oversight Committee shall have no authority to alter, modify or amend any of the rights and obligations of the Parties set forth under this Amended and Restated Research Agreement. If the Oversight Committee is unable to resolve any dispute, controversy, or claim with respect to items (A) – (G) above in this Section 2.3(f)(i) within thirty (30) days after it first addresses such matter (or such longer period as the Parties may mutually agree upon), then the dispute shall be referred to Executives of each Party. For purposes of clarification, all matters related to “technical aspects” of an approved Research Plan shall be resolved in accordance with Section 2.2(f)(i).

(ii) Decision Making Process If the Oversight Committee is Disbanded. If the Oversight Committee is disbanded by mutual agreement of the Parties prior to the expiration or termination of the Agreement pursuant to Section 2.3(h), then after such disbanding, decisions formerly within the jurisdiction of the Oversight Committee shall be submitted for resolution by designated Executives of each Party, subject to the decision making processes and principles set forth in Section 2.3(f)(i) as if Section 2.3(f)(i) applied to decisions to be made by such Executives.

(g) Expenses. Shell and Codexis shall each bear all expenses of their respective members related to their participation on the Oversight Committee.

(h) Disbanding of the Oversight Committee. The Parties shall have the right to disband the Oversight Committee upon mutual agreement. Failure to agree to disband the Oversight Committee shall not constitute a breach of this Agreement, nor trigger any Dispute Resolution process as described in Section 12.7. Additionally, the Oversight Committee shall be disbanded automatically upon the expiration or termination of the Agreement as set forth in Article 11.

2.4 Reports and Materials.

(a) Reports.

(i) During the Term, each Party shall provide to the Research Committee:

(1) summary written reports within thirty (30) days after the end of each three (3) month period commencing on the Effective Date, describing such Party’s work and progress, if any, under the Research Plans;

(2) annual executive summaries within thirty (30) days after each anniversary of the Effective Date for each Research Plan for which work was performed during the relevant Contract Year;

(3) a comprehensive written report within thirty (30) days after completion of all work under each Research Plan, describing in detail the work accomplished by it under such Research Plan and discussing and evaluating the results of such work; and

(4) a comprehensive written report within thirty (30) days after the end of the Term, describing in detail the work accomplished by it under the Research Plans during the Term and discussing and evaluating the results of such work.

(ii) During the Term, the Research Committee shall provide a written meeting discussion summary report to the Oversight Committee of each meeting of the Research Committee within ten (10) business days after each such meeting.

(iii) Any report delivered to a Party hereunder shall be owned by the delivering Party; provided, however, all such reports shall be deemed to be Confidential Information of both Parties for purposes of Article 6.

(b) Materials. Codexis and Shell shall, during the Term, as a matter of course as described in the Research Plans, or upon each other’s written or oral request, furnish to each other samples of biochemical, biological or synthetic chemical materials which are part of Shell Technology, Codexis Technology or Program Technology which are necessary for each Party to carry out its responsibilities under the Research Plans.

2.5 Laboratory Facility and Personnel.

(a) Codexis shall provide suitable laboratory facilities, equipment and personnel for the work to be done by Codexis in carrying out the Research Plans. For purposes of clarification, except as set forth in Section 2.5(b) below, all fees and payments due to Codexis hereunder for the provision of laboratory facilities, equipment and personnel are set forth in Article 3 below.

(b) Shell shall be responsible, at Shell’s sole cost and expense, for providing suitable laboratory facilities, equipment and personnel for the work to be done by Shell at Shell facilities, if any, in carrying out the Research Plans; provided that from time to time during the Term after the second (2nd) anniversary of the Effective Date, upon the written agreement of the Parties, Codexis shall make commercially reasonable efforts to accommodate no more than four (4) Shell employees at Codexis’ facilities in Redwood City, California, for periods of up to six (6) months, at Shell’s sole cost and expense, in order to permit such Shell employees to carry out activities under the Research Plans; provided further, that any such Shell employee shall first execute a confidentiality agreement with Codexis acceptable to Shell and to Codexis prohibiting such Shell employee from using or disclosing confidential information of Codexis for any purpose other than as necessary to carry out activities under the Research Plans (such limitations on use and disclosure to include without limitation disclosure to or use for the benefit of Shell or any Shell Affiliate); provided further that Shell shall agree to serve as a surety as to, and with respect to any damages suffered by Codexis or its Affiliates as a result of the breach of the non-use and non-disclosure restrictions set forth in such confidentiality agreement by such Shell employee, including without limitation any breach that may occur after such Shell employee is no longer an employee of Shell; provided further that in a circumstance of a former employee of Shell, Codexis shall first pursue its full legal rights against such former employee and/or Third Party that caused any such damages to Codexis, before Codexis seeks any relief from Shell but, thereafter, will not be required to reassert against Shell any claim or demand previously asserted against such former employee and/or such Third Party that, in such previous action, was resolved in favor of Codexis.

2.6 Efforts.

(a) Each Party shall use commercially reasonable efforts during the Term to perform that part of the Program for which such Party is responsible pursuant to the terms and conditions of this Amended and Restated Research Agreement, and to complete such tasks in compliance with the schedule set forth in the applicable Research Plan.

(b) FTEs.

(i) Beginning on the Effective Date and ending on March 31, 2007, Codexis shall assign eight (8) FTEs to perform Codexis’ obligations under the Program, and to complete the tasks assigned to Codexis in the Research Plan for such period. The Parties acknowledge and agree that as of the Execution Date, Codexis has fulfilled its obligations under this Section 2.6(b)(i).

(ii) Beginning on April 1, 2007 and ending on October 31, 2007, Codexis shall assign twelve (12) FTEs to perform Codexis’ obligations under the Program, and to complete the tasks assigned to Codexis in the Research Plan for such period. The Parties

acknowledge and agree that as of the Execution Date, Codexis has fulfilled its obligations under this Section 2.6(b)(ii) for the period beginning on April 1, 2007 and ending on the Execution Date.

(iii) Subject to Section 2.6(c), after the first anniversary of the Effective Date, during the Term, Codexis shall assign, on or before the dates set forth in the table in this Section 2.6(b)(iii), below, no less than the corresponding number of FTEs set forth in the table in this Section 2.6(b)(iii), below, to perform Codexis’ obligations under the Program, and to complete the tasks assigned to Codexis in the Research Plans.


Total Number of FTEs		Date
24		November 1, 2007

48		April 1, 2008

72		August 1, 2008

Notwithstanding the foregoing, either Party, upon not less than thirty (30) days prior written notice, may extend, by up to sixty (60) days, the dates set forth under the heading “Date” in the table above in this Section 2.6(b)(iii); provided, however, that under no circumstances will the total delay of any such date be greater than sixty (60) days, whether the delay is requested by Shell, Codexis, or both.

(iv) In the event that Codexis has resources available to dedicate to an approved Research Plan in advance of the schedule set forth in Section 2.6(b)(iii), Codexis shall allocate such resources to the Program upon thirty (30) days advance written notice to Shell.

(c) Reduction in FTEs.

(i) During the period beginning on August 1, 2008 and ending on the third (3rd) anniversary of the Effective Date, Shell shall have the right to reduce the total number of FTEs assigned by Codexis to perform Codexis’ obligations under the Program by up to twelve (12) FTEs upon sixty (60) days advance notice.

(ii) After the third (3rd) anniversary of the Effective Date, Shell shall have the right to reduce the total number of FTEs assigned by Codexis to perform Codexis’ obligations under the Program upon advance notice; provided, however, that the number of FTEs that may be reduced will not be greater than as set forth in, and implemented after written notice thereof in accordance with, the table in this Section 2.6(c)(ii), below; provided, further, however, that no reductions may be noticed during the applicable standstill period set forth in this Section 2.6(c)(ii), below, immediately after an FTE reduction already noticed (each such period during which no subsequent notice may be given, a “Standstill Period”).


Number of FTEs that May Be Reduced	Standstill Period	Advance Notice Required
< 12	90 days	30 days

13 < 48	180 days	90 days

> 48	360 days	180 days

By way of example, if Shell elects to reduce the number of FTEs by twelve (12) FTEs or less, no additional reductions may be made by Shell during the ninety (90) day Standstill Period beginning on the date of advance written notice of such reduction election. Similarly, if Shell elects to reduce the number of FTEs by more than twelve (12) FTEs but less than or equal to forty-eight (48) FTEs, no additional reductions may be made by Shell during the one hundred eighty (180) day Standstill Period beginning on the date of advance written notice of such reduction election.

2.7 Approval of Research Plans. Prior to beginning work, Codexis shall provide a proposed Research Plan to Shell for each work stream. Shell may comment on, and may make recommendations to, such proposed Research Plan from Codexis. The Parties shall submit such proposed Research Plan to the Research Committee for consideration and recommendation to the Oversight Committee for approval.

2.8 Milestones.

(a) Year One Final Milestone. Shell acknowledges that, as of the Execution Date, Codexis has achieved the Year One Final Milestone.

(b) Annual Milestones. Prior to beginning work, Codexis shall provide a proposal to Shell for annual milestones for each work stream. The Parties shall submit such proposed milestones to the Research Committee for consideration and recommendation to the Oversight Committee for approval.

(c) Year Four Goal(s). Unless otherwise agreed by the Parties in writing, prior to March 1, 2009, Codexis shall provide a proposal to Shell for Program progress goal(s) to be achieved as of the fourth (4th) anniversary of the Effective Date (the “Year Four Goal(s)”). The Parties shall submit such proposed Year Four Goal(s) to the Research Committee for consideration and recommendation to the Oversight Committee for approval. For purposes of clarification, it is the intent of the Parties that the Year Four Goal(s) will be more technically challenging to achieve than the annual Milestones established in accordance with Section 2.8(b).

(d) Year Six Goal(s). Unless otherwise agreed by the Parties in writing, prior to March 1, 2010, Codexis shall provide a proposal to Shell for Program progress goal(s) to be achieved as of the sixth (6th) anniversary of the Effective Date (the “Year Six Goal(s)”). The Parties shall submit such proposed Year Six Goal(s) to the Research Committee for consideration and recommendation to the Oversight Committee for approval. For purposes of

clarification, it is the intent of the Parties that the Year Six Goal(s) will be more technically challenging to achieve than the annual Milestones established in accordance with Section 2.8(b).

(e) Milestone Verification.

(i) In the event that Codexis reasonably believes that it has achieved a particular annual Milestone, the Year Four Goal(s) or the Year Six Goal(s), Codexis shall deliver written notice thereof to Shell (each such notice, a “Milestone Notice”). Within ten (10) business days after delivery of a particular Milestone Notice, Codexis shall provide to Shell sufficient quantities of any relevant Biocatalyst to permit Shell to verify that the annual Milestone, Year Four Goal(s) or Year Six Goal(s), as the case may be, in such Milestone Notice has been achieved.

(ii) In the event that Shell cannot verify Codexis’ assertion that Codexis has achieved the annual Milestone, Year Four Goal(s) or Year Six Goal(s), as the case may be, identified in a particular Milestone Notice, Shell shall provide written notice thereof to Codexis (each such notice, a “Nonreplication Notice”). The annual Milestone, Year Four Goal(s) or Year Six Goal(s), as the case may be, identified in each Milestone Notice shall be deemed to have been achieved unless Shell provides a Nonreplication Notice within ninety (90) days after Shell’s receipt of such Milestone Notice; provided that upon written notice provided prior to the expiration of such ninety (90) day period, Shell may seek an extension of such ninety (90) day period of up to forty-five (45) days to provide such Nonreplication Notice, not to be unreasonably withheld by Codexis. Upon Codexis’ receipt of a Nonreplication Notice, the Parties will determine a mutually agreeable time to perform the applicable tests necessary to replicate the identified annual asserted Milestone, Year Four Goal(s) or Year Six Goal(s), as the case may be, that is the subject of such Nonreplication Notice, such tests to be performed, at Shell’s sole option and expense (1) by Shell at a Shell facility, with Codexis observing; (2) by Codexis at a Codexis facility, with Shell observing; or (3) by a mutually agreeable Third Party at such Third Party’s facilities, with both Codexis and Shell observing. The outcome of such test shall be determinative of whether the annual Milestone, Year Four Goal(s) or Year Six Goal(s), as the case may be, has been achieved. In the event that Shell elects to have such test performed by a mutually agreeable Third Party, Codexis shall first execute a sponsored research agreement with such Third Party substantially in the form attached hereto as Exhibit 2.8(e)(ii).

ARTICLE 3

FEES AND PAYMENTS

3.1 Codexis Technology Access Fee. In consideration of the use of Codexis’ Technology and Codexis’ related technical knowledge and expertise during the first (1st) Contract Year of the Term, Shell shall pay to Codexis a non-refundable, non-creditable technology access fee of Xxx Xxxxxxx Xxxxx Xxxxxxx Xxxxxxxx Xxxxxx Xxxxxx Dollars ($2,800,000) on the Effective Date. The Parties acknowledge and agree that, as of the Execution Date, such technology access fee has been fully (a) earned by Codexis and (b) paid by Shell.

3.2 Exclusivity Fee. During the Term, Codexis (a) will act exclusively with Shell regarding the rights and research described herein; and (b) will not (i) conduct research, discover

or develop Biocatalysts, and associated processes for the use of such Biocatalysts, in the Field of Use for any other party or (ii) enter into any other agreements to conduct research, discover or develop Biocatalysts, and associated processes for the use of such Biocatalysts, in the Field of Use (including without limitation any agreement to convert Biomass to fermentable sugars unless such other party has provided express assurance in a written agreement that such fermentable sugars shall be used only outside the Field of Use), as more fully described with respect to both (a) and (b) in this Amended and Restated Research Agreement and pursuant to the covenant in Section 9.3. In consideration of such research activities performed exclusively for Shell in the Field of Use, Shell shall pay to Codexis an exclusivity fee of Twenty Million United States Dollars ($20,000,000) on the Execution Date. Except as expressly provided in Section 11.4(a), such exclusivity fee shall be non-refundable and non-creditable. For purposes of clarification, Shell acknowledges and agrees that such covenant regarding such exclusivity shall expire upon termination or expiration of this Agreement; provided that in the event of any Renewal Term in accordance with Section 11.1, Shell shall not be required to pay any additional exclusivity fee beyond that set forth in this Section 3.2 in order to maintain the research exclusivity as described herein and in Section 9.3 for the duration of this Agreement, including during the Initial Term and any such Renewal Term.

3.3 FTE Payments.

(a) First Contract Year. During the first (1st) Contract Year of the Term, Shell shall pay to Codexis a research funding fee based on an FTE rate equal to Four Hundred Thousand United States Dollars ($400,000) per year for each of the FTEs assigned by Codexis to perform Codexis’ obligations under the Program during such first (1st) Contract Year. Such FTE rate includes any and all associated overhead expenses, normal laboratory supplies and consumables expenses, and typical operational research expenses. The Parties acknowledge and agree that, as of the Execution Date, the FTE payments for the first (1st) Contract Year of the Term have been paid by Shell.

(b) After the First Contract Year. During the second (2nd) Contract Year of the Term, Shell shall pay to Codexis a research funding fee based on an FTE rate equal to Four Hundred Twenty Thousand United States Dollars ($420,000) per year for each of the FTEs assigned by Codexis to perform Codexis’ obligations under the Program during the second (2nd) Contract Year of the Term. Such FTE rate shall be increased annually at the beginning of each subsequent Contract Year of the Term by an amount equal to five percent (5%) of the FTE rate for the preceding Contract Year. Such FTE rate includes any and all associated overhead expenses, normal laboratory supplies and consumables expenses, and typical operational research expenses. Such FTE payments in each Contract Year shall be made in six (6) equal installments (each an “FTE Installment”), each in advance of work actually performed based on the planned utilization of FTEs for the following two (2) months; provided, however, that, in the event either Party elects to reduce the number of FTEs working on the Program pursuant to Section 2.6(c), a corresponding reduction will be made to the amount of the next FTE Installment. In the event that Codexis dedicates FTEs to the Program in advance of the schedule set forth in Section 2.6(b)(iii) in accordance with Section 2.6(b)(iv), Shell shall make an additional payment to Codexis on or before the date such increase shall become effective, which amount shall be equal to (i) the then-current FTE rate, times (ii) the number of additional FTEs,

times (iii) the number of days until the date on which the next FTE Installment is required to be paid pursuant to this Section 3.3(b), above, divided by (iv) three hundred sixty-five (365).

3.4 Milestone Payments.

(a) Shell shall pay to Codexis a one-time, non-refundable, non-creditable milestone payment equal to [*] within thirty (30) days after the receipt by Shell of the report due from Codexis at six (6) months after the Effective Date, as provided in Section 2.4(a)(i)(1). The Parties acknowledge and agree that, as of the Execution Date, such Milestone payment has been fully (i) earned by Codexis and (ii) paid by Shell.

(b) For each Contract Year during the Initial Term beginning with the third (3rd) Contract Year, Shell shall pay to Codexis a non-refundable, non-creditable Milestone payment equal to [*] (for a total of [*]) upon achievement of the Milestones for each of the then-current Research Plans established in accordance with Section 2.8(b), such amount to be distributed equally among all such then-current Research Plans. By way of example, if there are five (5) Research Plans in a Contract Year and Codexis achieves the Milestone established for each of three (3) of the five (5) Research Plans before the end of such Contract Year, Shell shall pay to Codexis a payment equal to [*] for that Contract Year; provided that, if Codexis achieves the Milestones established for the fourth (4^th) or fifth (5^th) Research Plans after such Contract Year and before the three (3) month anniversary of the expiration of such Contract Year, Shell shall pay Codexis a payment equal to [*] for each such Milestone after such Milestone has been achieved. For purposes of clarification, for purposes of this Section 3.4(b), “achievement of the applicable Milestone” means that Codexis delivers to Shell a Milestone Notice for such Milestone within the relevant time period, even if the verification of such Milestone Notice occurs after the expiration of such time period; provided, however, that payment for any Milestone due pursuant to this Section 3.4(b) will be due and payable in accordance with Section 3.6 only after the achievement of such Milestone has been verified in accordance with Section 2.8(e).

(c) Upon the achievement of the Year Four Goal(s), Shell shall pay to Codexis a one-time, non-refundable, non-creditable Milestone payment equal to [*]; provided, however, that payment for the Year Four Goal(s) due pursuant to this Section 3.4(c) will be due and payable in accordance with Section 3.6 only after the achievement of such Year Four Goal(s) has been verified in accordance with Section 2.8(e).

(d) Upon the achievement of the Year Six Goal(s), Shell shall pay to Codexis a one-time, non-refundable, non-creditable Milestone payment equal to [*]; provided, however, that payment for the Year Six Goal(s) due pursuant to this Section 3.4(d) will be due and payable in accordance with Section 3.6 only after the achievement of such Year Six Goal(s) has been verified in accordance with Section 2.8(e).

(e) For each Contract Year, if any, of (i) the Initial Term beyond the sixth (6th) Contract Year in the event that the Parties agree to extend the Initial Term beyond the six (6) year anniversary of the Effective Date in accordance with Section 11.1, and (ii) each Renewal Term, Shell shall pay to Codexis a non-refundable, non-creditable Milestone payment equal to [*] upon achievement of the Milestones for each of the then-current Research Plans established

in accordance with Section 2.8(b), such amount to be distributed equally among all then-current Research Plans. By way of example, if there are five (5) Research Plans in a Contract Year and Codexis achieves the Milestone established for each of three (3) of the five (5) Research Plans before the end of such Contract Year, Shell shall pay to Codexis a payment equal to [*] for that Contract Year; provided that, if Codexis achieves the Milestones established for the fourth (4^th) or fifth (5^th) Research Plans after such Contract Year and before the expiration of this Agreement, Shell shall pay Codexis a payment equal to [*] for each such Milestone after such Milestone has been achieved. For purposes of clarification, for purposes of this Section 3.4(e), “achievement of the applicable Milestone” means that Codexis delivers to Shell a Milestone Notice for such Milestone within the relevant time period, even if the verification of such Milestone Notice occurs after the expiration of such time period; provided, however, that payment for any such Milestone due pursuant to this Section 3.4(e) will be due and payable in accordance with Section 3.6 only after the achievement of such Milestone has been verified in accordance with Section 2.8(e).

3.5 Equity Payments.

(a) Series D Stock Purchase Agreement. Upon the Effective Date, Shell shall purchase Three Million United States Dollars ($3,000,000) of Series D Preferred Stock of Codexis, pursuant to the terms and conditions of a stock purchase agreement in the form attached hereto as Schedule A, appended to and made part of this Amended and Restated Research Agreement, (the “Series D Stock Purchase Agreement”) at Three United States Dollars and Ninety-Seven Cents ($3.97) per share. The Parties acknowledge and agree that, as of the Execution Date, such Series D Preferred Stock has been (i) issued to Shell by Codexis and (ii) paid for in full by Shell.

(b) Series E Stock Purchase Agreement. On or before the Execution Date, Shell shall purchase a sufficient number of shares of Series E Preferred Stock of Codexis, pursuant to the terms and conditions of a stock purchase agreement substantially in the form attached hereto as Schedule B, appended to and made part of this Amended and Restated Research Agreement, (the “Series E Stock Purchase Agreement”) at Eight United States Dollars and Fifty Cents ($8.50) per share, such that immediately after such purchase, Shell shall own ten percent (10.0%) of the equity securities of Codexis on a fully diluted basis; provided that at each Subsequent Closing (as defined in the Series E Stock Purchase Agreement), if any, Shell shall purchase an additional number of shares of Series E Preferred Stock such that immediately after each such Subsequent Closing Shell shall own ten percent (10.0%) of the equity securities of Codexis on a fully diluted basis. Notwithstanding anything to the contrary, the Parties acknowledge and agree that the maximum amount that Shell shall be required to invest under the Series E Stock Purchase Agreement shall be Thirty Million Seven Hundred Three Thousand Five Hundred Sixty-Four United States Dollars ($30,703,564). For purposes of this Section 3.5(b) only, “fully diluted basis” means all shares of Codexis common stock then outstanding, assuming full exercise and/or conversion of all outstanding Codexis securities exercisable and/or convertible into Codexis common stock and including shares reserved for issuance in connection with options not yet granted under any Codexis equity incentive plan.

(c) On or before the Execution Date, Shell will exercise, in full, the Warrant Agreement.

3.6 Mode of Payment. All payments made pursuant to this Amended and Restated Research Agreement, other than those due on the Execution Date or the Effective Date or under Section 5.2, shall be due and payable within sixty (60) days following receipt by Shell of a relevant invoice from Codexis. Such payments shall be made by direct wire transfer of United States Dollars in immediately available funds in the requisite amount to such bank account as Codexis may from time to time designate by written notice to Shell. Payments will be free and clear of any taxes (and net of any withholding and other taxes imposed on the payee), fees or charges, to the extent applicable.

3.7 Late Payment Interest. Any payment due and payable to Codexis under the terms and conditions of Section 3.3, 3.4, or 5.2 made by Shell later than sixty (60) days after the date such payment is due and payable shall bear interest as of the day after the date such payment was due and payable and shall continue to accrue such interest until such payment is made at a rate equal to the lesser of either (a) two percent (2%) above the prime rate as reported by Citibank, New York, New York, as of the date such payment was due and payable, or (b) the maximum rate permitted by applicable law. The Parties acknowledge and agree that, as of the Execution Date, there are no outstanding late payments due to Codexis that would be subject to interest payments pursuant to this Section 3.7.

ARTICLE 4

INTELLECTUAL PROPERTY RIGHTS

4.1 Ownership.

(a) Shell Technology. Subject to the rights expressly granted to Codexis under the terms and conditions of this Amended and Restated Research Agreement and the Amended and Restated License Agreement, Shell or its Affiliates owns or otherwise controls and shall own or otherwise control all right, title and interest in, to and under any and all Shell Technology.

(b) Codexis Technology. Subject to the rights expressly granted to Shell under the terms and conditions of this Amended and Restated Research Agreement and the Amended and Restated License Agreement, Codexis owns or otherwise controls and shall own or otherwise control all right, title and interest in, to and under any and all Codexis Technology.

(c) Program Technology. Subject to the rights expressly granted to Shell under the terms and conditions of this Amended and Restated Research Agreement and the Amended and Restated License Agreement, Codexis owns or otherwise controls and shall own or otherwise control all right, title and interest in, to and under any and all Program Technology.

4.2 Grant of Research Licenses.

(a) Codexis grants to Shell a non-exclusive, irrevocable, worldwide, royalty-free license, including the right to grant sublicenses to its Affiliates, to make and use Codexis Technology and Program Technology solely to conduct activities in accordance with Shell’s responsibilities, to be articulated under each Research Plan; provided, however, that this license does not include and Shell shall not acquire, by virtue of this license, any rights in, to or under the Shuffling Technology.

(b) Shell grants to Codexis a non-exclusive, irrevocable, worldwide, royalty-free license, including the right to grant sublicenses to its Affiliates, to make and use Shell Technology solely to conduct activities in accordance with Codexis’ responsibilities, to be articulated under each Research Plan.

4.3 Limitation. Except as expressly provided in this Amended and Restated Research Agreement and the Amended and Restated License Agreement, no right, title or interest is granted by either Party to the other Party.

ARTICLE 5

PATENT PROSECUTION AND MAINTENANCE

5.1 Filing, Prosecution and Maintenance by Codexis. With respect to the Program Patent Rights arising from the Program, Codexis shall have the right, but not an obligation to:

(a) file applications for letters patent on any invention included in such Patent Rights;

(b) take all reasonable steps to prosecute all pending and new patent applications included within such Program Technology;

(c) respond to oppositions, nullity actions, re-examinations, revocation actions and similar proceedings filed by Third Parties against the grant of letters patent for such applications; and

(d) maintain in force any letters patent included in such Patent Rights by duly filing all necessary papers and paying any fees required by the patent laws of the particular country in which such letters patent were granted.

In addition, Codexis shall have the right, but not the obligation, to initiate and prosecute oppositions, nullity actions, re-examinations, revocation actions and similar proceedings against the grant of letters patent owned by Third Parties that may limit the ability of the Parties to exploit the Program Technology.

Notwithstanding the foregoing, Codexis shall consult with Shell regarding countries in which such patent applications or issued patents, as applicable, should be filed, prosecuted, and/or maintained. If Codexis agrees to file, prosecute, and/or maintain such patent applications or issued patents, as applicable, Codexis shall do so as set forth in this Section 5.1, above, in those countries where Shell requests that Codexis file, prosecute, and/or maintain such applications;

provided that Codexis, at its option and exercise, may file prosecute, and/or maintain applications in countries where Shell does not request that Codexis file, prosecute, and/or maintain such applications. If Codexis does not agree to file, prosecute, and/or maintain such patent applications or issued patents, as applicable, Codexis shall provide Shell with written notice of any decision to not file a patent application or to abandon a pending application or an issued patent included in such Patent Rights, such notice to be delivered at least thirty (30) days prior to any action required to obtain or maintain such pending application or such issued patent, as the case may be. Thereafter, Shell shall have the option, at its expense, of filing such an application, or continuing to prosecute any such pending patent application or of keeping the issued patent in force, as applicable. In the event that Shell exercises such option for any such pending application or such issued patent, Codexis shall assign to Shell such pending application or such issued patent, as the case may be. Codexis shall cooperate fully with, and take all necessary actions requested by, Shell in connection with the preparation, prosecution and maintenance of any such letters patent included in such Patent Rights.

5.2 Reimbursement of Costs for Filing, Prosecuting and Maintaining Patent Rights. Within thirty (30) days after receipt of an invoice from Codexis, Shell shall reimburse Codexis for a portion of the costs of (a) filing, prosecuting, responding to opposition and maintaining patent applications and patents in countries where Shell requests that patent applications be filed, prosecuted and maintained, and (b) filing, prosecuting, and responding to oppositions, nullity actions, re-examinations, revocation actions and similar proceedings against the grant of letters patent owned by Third Parties that may limit the ability of the Parties to exploit the Program Technology. Such reimbursement shall equal fifty percent (50%) of such costs actually incurred in the United States, Europe, Argentina, Australia, Brazil, China, India, Japan, Singapore, South Korea and Turkey, and one hundred percent (100%) of such costs elsewhere, and in each case, shall be in addition to payments under Article 3. However, Shell may, upon sixty (60) days notice, request that Codexis discontinue filing or prosecution of patent applications in any country and shall have no obligation after the effective date of such notice to reimburse Codexis for the costs of filing, prosecuting, responding to opposition or maintaining such patent application or patent in such country. Codexis shall pay all costs in those countries in which Shell does not request that Codexis file, prosecute or maintain patent applications and patents, but in which Codexis, at its option, elects to do so.

ARTICLE 6

CONFIDENTIALITY

6.1 Confidentiality Obligations. The Parties agree that, during the Term and for five (5) years thereafter, all Confidential Information disclosed by one Party to the other Party hereunder shall be received and maintained by the receiving Party in strict confidence, shall not be used for any purpose other than the purposes expressly permitted by this Amended and Restated Research Agreement, and shall not be disclosed to any Third Party. The Parties acknowledge and agree that the structure and composition of each particular Biocatalyst developed under the Program shall be deemed Confidential Information of Codexis, subject to the confidentiality and non-use obligations set forth in this Article 6. Shell shall limit the disclosure of Third Party Information to Codexis to that required for the Program. No Third

Party Information shall be disclosed until (i) Shell has described the general nature and scope of the information to be disclosed and the terms and conditions attaching to disclosure and use; and (ii) Codexis has agreed to receive such information in confidence under such terms and conditions. The obligations of confidentiality and non-use set forth in the first sentence of this Section 6.1 will not apply to any information to the extent that it can be established by the receiving Party that such information:

(a) was already known to the receiving Party or its Affiliates at the time of disclosure without restriction as to confidentiality or use, as evidenced by competent evidence;

(b) was generally available to the public or was otherwise part of the public domain at the time of its disclosure to the receiving Party or its Affiliates;

(c) became generally available to the public or otherwise becomes part of the public domain after its disclosure and other than through any fault of the receiving Party or its Affiliates in breach of this Amended and Restated Research Agreement;

(d) was subsequently lawfully disclosed to the receiving Party or its Affiliates by a Third Party without restriction as to confidentiality or use and other than in contravention of a confidentiality obligation of such Third Party to the disclosing Party or its Affiliates; or

(e) is independently developed by employees or agents of the receiving Party or its Affiliates without reliance upon or access to Confidential Information of the disclosing Party or its Affiliates, as evidenced by competent evidence.

Each Party represents and warrants that it has or will obtain written agreements from each of its consultants who perform work on the Program or otherwise have a need to know the other Party’s Confidential Information, which agreements will obligate such persons to obligations of confidentiality and non-use no less restrictive than those assumed by the Parties herein, and to assign to such Party all inventions made by such persons during the course of performing any tasks associated with the Program. Further, each Party represents and warrants that those of its employees which perform work on the Program or otherwise have a need to know the other Party’s Confidential Information are bound by obligations of confidentiality and non-use to the employer Party. Either Party may disclose Confidential Information of the other Party to such Party’s Affiliates, provided that any such Affiliate agrees prior to such disclosure to be bound by obligations of confidentiality and non-use no less restrictive than those assumed by such disclosing Party herein.

Notwithstanding this Article 6 the receiving Party may disclose any Confidential Information of the disclosing Party that the receiving Party is required to disclose under applicable laws or regulations or an order by a court or other regulatory body having competent jurisdiction; provided, however, that except where impracticable, the receiving Party shall give the disclosing Party reasonable advance notice of such disclosure requirement (which shall include a copy of any applicable subpoena or order) and shall afford the disclosing Party a reasonable opportunity to oppose, limit or secure confidential treatment for such required disclosure. In the event of any such required disclosure, the receiving Party shall disclose only that portion of the Confidential Information of the disclosing Party that the receiving Party is legally required to disclose and, in

the event a protective order is obtained by the disclosing Party, nothing in this Article 6 shall be construed to authorize the receiving Party to use or disclose any disclosing Party Confidential Information to parties other than such court or regulatory body or beyond the scope of the protective order. Codexis and its Affiliates may disclose this Amended and Restated Research Agreement if required to be disclosed by applicable State or federal tax or securities laws to the extent, and only to the extent, such laws require such disclosure and Codexis provides Shell a reasonable opportunity to review and comment on the general text of such disclosure.

6.2 Press Releases. Except to the extent required by law or regulation or as otherwise permitted in accordance with this Section 6.2, no Party shall make any public announcements concerning this Amended and Restated Research Agreement or the terms hereof without the prior written consent of the other Party and the Parties shall agree on the content and timing of any such public announcement. Notwithstanding the foregoing, the Parties will issue a mutually acceptable joint press release within sixty (60) days after the first anniversary of the Effective Date.

ARTICLE 7

ACQUISITION OF RIGHTS FROM THIRD PARTIES

7.1 Acquisition of Rights from Third Parties. In the event that during the Term, either Party makes a determination that there may be an opportunity to acquire technology or patents or information from a Third Party that may be useful in the Program (collectively, the “Acquired Technology”), such Party, at its sole discretion, will notify the other Party thereof through the Research Committee. Codexis and Shell shall decide, considering the recommendations of the Research Committee and the Oversight Committee, if such rights of a Third Party should be acquired in connection with the Program and, if so, whether by Codexis, Shell or both. If acquired, such rights shall become part of the Confidential Information, Technology or Patent Rights, whichever is appropriate, of the acquiring Party or Parties. Notwithstanding anything to the contrary, the decision to acquire such rights shall not be considered a “technical aspect” for purposes of section 2.2(f) of this Restated and Amended Research Agreement.

7.2 Payments. [*] for payments owed by [*] to any Third Party in connection with any agreed acquisition of Acquired Technology pursuant to Section 7.1; provided that, [*] such Acquired Technology for purposes [*], the Parties shall first agree on the proportion of such payments to be [*] for the use of such Acquired Technology in the [*].

ARTICLE 8

OTHER AGREEMENTS

8.1 Amended and Restated License Agreement. Concurrently with the execution of this Amended and Restated Research Agreement, Codexis and Shell shall enter into the Amended and Restated License Agreement substantially in the form attached hereto as Schedule C, appended to and made part of this Amended and Restated Research Agreement.

8.2 Issuance of Warrants. On the Effective Date, Codexis issued a warrant agreement, as attached hereto as Schedule D, and appended to and made part of this Amended and Restated Research Agreement (the “Warrant Agreement”), wherein Codexis agreed to issue warrants for the purchase of Three Million United States Dollars ($3,000,000) of preferred stock by Shell at the following price per share, as more fully set forth in the Warrant Agreement:

(a) In the event that Codexis fails to achieve the Year One Final Milestone, the purchase price per share shall equal Three United States Dollars and Ninety-Seven Cents ($3.97); and

(b) In the event that Codexis achieves the Year One Final Milestone, the purchase price per share shall equal Seven United States Dollars ($7.00).

Notwithstanding anything to the contrary, Shell acknowledges that the Year One Final Milestone has been achieved for purposes of this Section 8.2(b). On or before the Execution Date, Shell will exercise, in full, the Warrant Agreement.

8.3 Entire Agreement. This Amended and Restated Research Agreement, the Amended and Restated License Agreement, the Series D Stock Purchase Agreement, and the Series E Stock Purchase Agreement are the sole agreements with respect to the subject matter hereof and supersede all other prior and contemporaneous agreements and understandings between the Parties with respect to same, including without limitation that certain Non-Binding Term Sheet by and between Codexis and Shell dated as of August 23, 2006, that certain Collaborative Research Agreement by and between Codexis and Shell effective as of November 1, 2006, as amended, and that certain License Agreement by and between Codexis and Shell effective as of November 1, 2006.

ARTICLE 9

REPRESENTATIONS AND WARRANTIES

9.1 Representations by Codexis. Codexis represents and warrants that, as of the Execution Date: (a) it is duly organized and validly existing under the laws of the jurisdiction of its incorporation and has full corporate power and authority to enter into this Amended and Restated Research Agreement; (b) it is in good standing with all relevant governmental authorities; (c) it has taken all corporate actions necessary to authorize the execution and delivery of this Amended and Restated Research Agreement and the performance of its obligations under this Amended and Restated Research Agreement; (d) the performance of its obligations under this Amended and Restated Research Agreement do not conflict with, or constitute a default under its charter documents, any contractual obligation of Codexis or any court order; (e) it Controls the Codexis Technology and it has the right to make the grants set forth in this Amended and Restated Research Agreement; (f) it is not aware of, and has not been served with, any suit or action pending in any court against Codexis, alleging patent infringement based on the use of Codexis Technology by Codexis or any Affiliate or licensee of Codexis, and Codexis has not received any communications or notice alleging any such patent infringement; and (g) it has not (i) provided any Third Party, including the United States government or agency thereof, any claim to rights relating to the Codexis Technology or the Program Technology, or (ii) entered

into any agreements, commitments or other arrangement with any Third Party, including the United States government or agency thereof, in each case that would (1) prohibit Codexis from fulfilling its obligations hereunder or (2) be inconsistent or in conflict with the rights granted to Shell hereunder.

9.2 Representations by Shell. Shell represents and warrants that, as of the Execution Date: (a) it is duly organized and validly existing under the laws of the jurisdiction of its formation and has full corporate power and authority to enter into this Amended and Restated Research Agreement; (b) it is in good standing with all relevant governmental authorities; (c) it has taken all corporate actions necessary to authorize the execution and delivery of this Amended and Restated Research Agreement and the performance of its obligations under this Amended and Restated Research Agreement; (d) the performance of its obligations under this Amended and Restated Research Agreement does not constitute either a default under its charter documents or a violation of any court order; and (e) it or one of its Affiliates Controls the Shell Technology and it has the right to make the grants set forth in this Amended and Restated Research Agreement.

9.3 Covenants of Codexis. Codexis covenants that, during the Term, without the prior written consent of Shell, it (a) will act exclusively with Shell regarding the rights and research described herein; (b) will not (i) conduct research, discover or develop biocatalysts, and associated processes for the use of such biocatalysts, in the Field of Use for any other party or (ii) enter into any other agreements to conduct research, discover or develop biocatalysts, and associated processes for the use of such biocatalysts, in the Field of Use (including without limitation any agreement to convert Biomass to fermentable sugars unless such other party has provided express assurance in a written agreement that such fermentable sugars shall be used only outside the Field of Use); (c) will maintain technical personnel with sufficient skill, experience and expertise to perform its obligations under the Program; and (d) will not (i) provide any Third Party, including the United States government or agency thereof, any claim to rights relating to the Codexis Technology or the Program Technology, or (ii) enter into any agreements, commitments or other arrangement with any Third Party, including the United States government or agency thereof, in each case that would (1) prohibit Codexis from fulfilling its obligations hereunder or (2) be inconsistent or in conflict with the rights granted to Shell hereunder. Codexis further covenants that, during the Term, (A) Codexis will provide written notice to Shell in the event that Codexis has a bona fide business opportunity with a Third Party available to Codexis that would involve the conversion of Biomass into fermentable sugars, such sugars to be used to generate product(s) outside the Field of Use and, to the extent that Codexis is not precluded, whether by confidentiality obligations or other similar restrictions, Codexis shall inform Shell of the name of such Third Party and such product(s) outside the Field of Use; and (B) in the event that Codexis reasonably believes that any Third Party with which Codexis entered into an agreement in accordance with Section 9.3(b)(ii) above is practicing intellectual property owned or otherwise controlled by Codexis to convert Biomass to fermentable sugars, where such sugars are being used in the Field of Use for the benefit of such Third Party or any party other than Shell or a Shell Affiliate, Codexis shall take reasonable steps, including appropriate legal action, to enforce its rights to stop such use.

9.4 Covenants of Shell. Shell covenants that it will not, without the prior written consent of Codexis, (a) reverse engineer, deconstruct or in any way determine, or attempt to reverse engineer, deconstruct or in any way determine, the structure or composition of any Biocatalyst developed by Codexis hereunder, except as expressly provided under 7.3(a) of the Amended and Restated License Agreement for any particular identified Biocatalyst; or (b) modify or otherwise create any derivative of any such Biocatalyst; or (c) do indirectly, either through a Third Party or a Shell Affiliate, any of the activities contained in (a) or (b) above that Shell itself agrees not to do. Notwithstanding the foregoing, in the event that Shell desires to modify or otherwise create any derivative of any Biocatalyst developed by Codexis hereunder and Codexis notifies Shell in writing within one hundred twenty (120) days after receipt by Codexis of a written request by Shell to modify or otherwise create any derivative of any such Biocatalyst that it is unwilling or unable to perform such modification or otherwise create such derivative under commercially reasonable terms, then Shell shall be relieved of its obligations under this Section 9.4 with respect to such Biocatalyst.

9.5 Disclaimer of Warranties. EXCEPT AS SPECIFICALLY SET FORTH IN THIS ARTICLE 9, NEITHER PARTY MAKES ANY REPRESENTATION OR WARRANTY, EXPRESS OR IMPLIED, INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE OR USE, NON-INFRINGEMENT, AND ANY OTHER STATUTORY WARRANTY.

ARTICLE 10

INDEMNIFICATION

10.1 Employees and Property. Each of Codexis and Shell (each, the “Indemnitor”) shall indemnify, defend and hold the other Party and its Affiliates and their respective agents, employees, consultants, officers and directors (the “Indemnitees”) harmless from and against any and all liability, damage, loss, cost or expense (including reasonable attorneys’ fees) (collectively “Losses”), arising from any claims or suits arising from (a) bodily injuries, including fatal injury or disease, to the Indemnitor’s employees, and (b) damage to tangible, real or personal property of Indemnitor and/or Indemnitor’s employees arising from or in connection with the performance of this Amended and Restated Research Agreement. THIS INDEMNITY SHALL APPLY IN FULL EVEN THOUGH THE CAUSE OF THE INJURIES, LOSS OR DAMAGE WAS THE NEGLIGENCE OF THE INDEMNITEE OR THE INDEMNITEE’S REPRESENTATIVES.

10.2 Third Parties.

(a) Indemnification by Codexis: Codexis shall indemnify, defend and hold the Shell Indemnitees harmless from and against any and all Losses arising out of any Third Party claims or suits arising from: (i) breach by Codexis of any of its representations, warranties or covenants under this Amended and Restated Research Agreement; or (ii) Codexis’ failure to perform its obligations under this Amended and Restated Research Agreement; or (iii) during the Term, infringement of patent rights owned or otherwise controlled by such Third Party as a result of Codexis’ research activities under this Amended and Reseated Research Agreement; provided that Codexis’ indemnification obligations pursuant to this Section 10.2(a)(iii) shall not extend to

any such Loss that arises from Codexis’ activities with respect to intellectual property provided to Codexis or any Affiliate of Codexis by or on behalf of Shell or any Affiliate of Shell, or to such activities with respect to improvements made by Codexis or any Affiliate of Codexis to such intellectual property under the Program; or (iv) the negligence, willful misconduct or strict liability of Codexis or its Affiliates, and its or their directors, officers, agents, employees, sublicensees or consultants; except in any such case for Losses to the extent, and only to the extent, reasonably attributable to a breach by Shell of its representations and warranties set forth in this Amended and Restated Research Agreement or the Shell Indemnitees having committed an act or acts of gross negligence, recklessness or willful misconduct. For purposes of clarification, the Parties acknowledge and agree that Codexis’ indemnification obligations pursuant to Section 10.2(a)(iii) shall not apply to any liability, damage, loss, cost or expense (including attorneys’ fees) as a result of any activities conducted under the Amended and Restated License Agreement.

(b) Indemnification by Shell: Shell shall fully indemnify, defend and hold the Codexis Indemnitees harmless from and against any and all Losses arising out of any Third Party claims or suits arising from: (i) breach by Shell of its representations, warranties or covenants under this Amended and Restated Research Agreement; or (ii) Shell’s failure to perform its obligations under this Amended and Restated Research Agreement; or (iii) the use under this Amended and Restated Research Agreement by Shell of any Biocatalyst except to the extent such Losses relate to the infringement of any intellectual property right of a Third Party; or (iv) infringement of patent rights owned or otherwise controlled by such Third Party as a result of intellectual property provided to Codexis or any Affiliate of Codexis by or on behalf of Shell or any Affiliate of Shell, or to such activities with respect to improvements made by Codexis or any Affiliate of Codexis to such intellectual property under the Program; or (v) the negligence, willful misconduct or strict liability of Shell or its Affiliates, and its or their directors, officers, agents, employees, sublicensees or consultants; or (v) the activities of Shell employees carrying out Research Plans in Codexis’ facilities pursuant to Section 2.5(b); except in any such case for Losses to the extent, and only to the extent, reasonably attributable to a breach by Codexis of its representations and warranties set forth in this Amended and Restated Research Agreement or the Codexis Indemnitees having committed an act or acts of gross negligence, recklessness or willful misconduct.

10.3 Environmental. Notwithstanding any other indemnification obligation in this Amended and Restated Research Agreement, and in addition to any rights the Parties may have under relevant federal, state, or local statutory and common laws, each Party shall fully indemnify, defend and hold the other Party and its Affiliates harmless from and against any and all Losses incurred as a result of Environmental Matters; provided, however, that this indemnification shall not apply to the extent any such Losses result from the acts or omissions of personnel of the indemnified Party or its Affiliates which occur at any site of the indemnified Party or the site of any supplier of the indemnified Party. For purposes of this Section 10.3, “Environment Matters” shall mean:

(a) the operation by the indemnifying Party, its Affiliates, sublicensees or subcontractors of any site or facility in a manner that is not in compliance with and in violation of any Environmental Law;

(b) any release of Hazardous Materials into the environment by the indemnifying Party, its Affiliates, sublicensees or subcontractors; or any Hazardous Materials that have been Disposed of at a site of the indemnifying Party or any site of any supplier (other than Codexis as supplier) of the indemnifying Party or other site or facility operated by the indemnifying Party, its Affiliates or its subcontractors, as the term Disposed is defined in applicable Environmental Laws;

(c) any failure to obtain or maintain all permits and provide all notices required by Environmental Laws for the lawful operation of any site of the indemnifying Party or any site of any supplier of the indemnifying Party or other facilities or sites operated by the indemnifying Party, its Affiliates, sublicensees or subcontractors; and

(d) any other actual or alleged act or omission relating to the handling or disposal of Hazardous Materials at any site of the indemnifying Party or any site of any supplier of the indemnifying Party or the handling or disposal of Hazardous Materials by the indemnifying Party, its Affiliates, sublicensees or subcontractors at any other facility or site.

For purposes of this Section 10.3, “Environmental Law” shall mean any treaty, law, ordinance, regulation or order of any jurisdiction, relating to environmental matters, including, but not limited to, matters governing air pollution; water pollution; the use, handling, reporting, release, storage, transport, or disposal of Hazardous Materials as defined herein above; exposure to or discharge of Hazardous Materials; occupational safety and health; and public health.

For purposes of this Section 10.3, “Hazardous Materials” includes, but is not limited to, air contaminant, water pollutant, hazardous material, hazardous waste, hazardous substance, toxic and hazardous substance, medical waste, infectious waste, “chemicals know to the State of California to cause cancer or reproductive toxicity”, asbestos and PCB’s, as such substances are defined under any applicable federal, state or local statute, regulation, rule or ordinance.

10.4 Notification of Claim; Conditions to Indemnification Obligations. As a condition to a Party’s right to receive indemnification under this Article 10, it shall: (a) promptly notify (“Claim Notice”) the other Party as soon as it becomes aware of a claim or suit for which indemnification may be sought pursuant hereto (provided that the failure to give a Claim Notice promptly shall not prejudice the rights of an indemnified Party except to the extent that the failure to give such prompt notice materially adversely affects the ability of the indemnifying Party to defend the claim or suit); (b) cooperate with the indemnifying Party in the defense of such claim or suit, at the expense of the indemnifying Party; and (c) if the indemnifying Party confirms in writing to the indemnified Party its intention to defend such claim or suit within fifteen (15) business days of receipt of the Claim Notice, permit the indemnifying Party to control the defense of such claim or suit, including without limitation the right to select defense counsel; provided that if the indemnifying Party fails to (i) provide such confirmation in writing within the fifteen (15) business day period; or (ii) diligently and reasonably defend such suit or claim at any time, its right to defend the claim or suit shall terminate immediately in the case of (i) and otherwise upon twenty (20) days’ written notice to the indemnifying Party and the indemnified Party may assume the defense of such claim or suit at the sole expense of the indemnifying Party and may settle or compromise such claim or suit without the consent of the

indemnifying Party. In no event, however, may the indemnifying Party compromise or settle any claim or suit in a manner which admits fault or negligence on the part of any indemnified Party or that otherwise materially affects such indemnified Party’s rights under this Amended and Restated Research Agreement or requires any payment by an indemnified Party without the prior written consent of such indemnified Party. Except as expressly provided above, the indemnifying Party will have no liability under this Article 10 with respect to claims or suits settled or compromised without its prior written consent. The indemnified Party shall have the right, but not the duty, at its sole cost and expense, to participate in the defense of any claim or suit hereunder with attorneys of its own selection without relieving the indemnifying Party of any of its obligations hereunder.

ARTICLE 11

TERM AND TERMINATION

11.1 Term. The initial term of this Amended and Restated Research Agreement will commence on the Effective Date and, unless earlier terminated in accordance with Section 11.2, 11.3, 12.2 or 12.4 below, shall continue in effect until six (6) years after the Effective Date (“Initial Term”); provided, however, that on or before the fourth (4th) anniversary of the Effective Date, the Parties will engage in discussions concerning the progress of the research under the Program, applicable future Milestones and Program needs, including the projected number of FTEs to complete the work under the Program, and the Parties shall determine whether the Initial Term will be extended under the same terms and conditions of this Restated and Amended Research Agreement. The term of this Amended and Restated Research Agreement may be extended after the Initial Term by consecutive, successive two (2) year periods (each, a “Renewal Term”) upon the mutual written agreement of the Parties at least six (6) months prior to the end of the Initial Term or the current Renewal Term, as applicable (the Initial Term, together with any and all Renewal Terms, the “Term”).

11.2 Termination for Convenience.

(a) At any time after the third (3rd) anniversary of the Effective Date, Shell may, in its sole discretion, terminate this Amended and Restated Research Agreement upon six (6) months written notice to Codexis.

(b) If at any time after the third (3rd) anniversary of the Effective Date, Shell determines, in accordance with Section 2.6(c), to decrease the number of FTEs assigned by Codexis to perform Codexis’ obligations under the Program to less than twenty-four (24), Codexis shall have the right, but not the obligation, to terminate this Amended and Restated Research Agreement upon ninety (90) days written notice to Shell; provided, however that in the event that (i) each such FTE reduction by Shell occurs after successful achievement of the applicable Milestone for each Research Plan and (ii) Shell (or a Shell Affiliate or sublicensee) is actively developing the Program Technology for commercial application, then Codexis shall have no right to terminate this Amended and Restated Research Agreement pursuant to this Section 11.2(b).

11.3 Termination Upon Material Breach. Material failure by a Party to comply with any of its obligations contained herein shall entitle the Party not in default to give to the Party in default written notice (a “Default Notice”) specifying the nature of the default in reasonable detail, requiring such defaulting Party to make good or otherwise cure such default, and stating the non-defaulting Party’s intention to terminate this Amended and Restated Research Agreement if such default is not cured. If such default is not cured within sixty (60) days after the date the Default Notice was sent, then the Party not in default shall be entitled, without prejudice to any other rights conferred on it by this Amended and Restated Research Agreement, and in addition to any other remedies available to it by law or in equity, to terminate this Amended and Restated Research Agreement by written notice of termination to the defaulting Party; provided, however, that if the Party receiving such Default Notice (the “Disputing Party”) has a reasonable basis for disputing that it is in default and such Party provides written notice thereof to the other Party before the expiration of such sixty (60) day cure period, then the Disputing Party shall have the right, prior to the expiration of such sixty (60) day period, to submit such dispute for resolution in accordance with the provisions of Section 12.7; provided further that in the event that as a result of such resolution, the Disputing Party is found to be in default and such default is not cured within forty-five (45) days after the date of such resolution, then the Party not in default shall be entitled, without prejudice to any other rights conferred on it by this Amended and Restated Research Agreement, and in addition to any other remedies available to it by law or in equity, to terminate this Amended and Restated Research Agreement by written notice of termination to the Disputing Party.

11.4 Consequences of Expiration or Termination.

(a) If Shell terminates this Amended and Restated Research Agreement pursuant to Section 11.3 (Material Breach), 12.2 (Assignment) or 12.4 (Force Majeure), or if Codexis terminates this Amended and Restated Research Agreement pursuant to Section 11.2(b) (Termination for Convenience), then (i) the Amended and Restated License Agreement shall continue according to its terms; and (ii) Codexis shall pay to Shell any amount previously paid to Codexis pursuant to Section 3.3 that, as of the effective date of such termination, has not been spent on performing Codexis’ obligations under the Program and does not correspond to a non-cancellable commitment with respect to such performance; provided, however, that in the event that Shell terminates this Amended and Restated Research Agreement prior to the sixth (6th) anniversary of the Effective Date pursuant to Section 11.3 (Material Breach), 12.2 (Assignment) or 12.4 (Force Majeure) (provided such termination pursuant to Section 12.4 occurs no sooner than nine (9) months after the applicable force majeure event and provided further that Codexis is the Party affected by such force majeure event and provides Shell with the full particulars thereof as soon as it becomes aware of the same (including its best estimate of the likely extent and duration of the interference with its activities), and Codexis can represent in good faith that it can resume its performance under this Amended and Restated Research Agreement, no later than nine (9) months after such force majeure event), Codexis shall refund the exclusivity fee paid by Shell to Codexis in accordance with Section 3.2 on a pro rata basis based on the quotient obtained by dividing (A) the duration of time remaining between the effective date of such termination and the sixth (6th) year anniversary of the Effective Date by (B) five (5) years. By way of example, if Shell terminates this Amended and Restated Research Agreement pursuant to

Section 11.3 on the fourth (4th) anniversary of the Effective Date, then Codexis shall refund Eight Million United States Dollars ($8,000,000) to Shell.

(b) The following Articles and Sections of this Amended and Restated Research Agreement shall survive its termination or expiration: Articles 4, 5, 10 and 12, and Sections 2.4(a)(iii), 6.1, 8.3, 9.4, 9.5 and 11.4.

(c) Termination of this Amended and Restated Research Agreement for any reason shall be without prejudice to (i) the rights and obligations of the Parties set forth in any Articles or Sections which provide by their terms performance by either Party subsequent to termination; (ii) Codexis’ rights to receive all payments accrued under Article 3 (subject to Section 11.4(a) above, if applicable), or (iii) any other remedies which either Party may otherwise have.

ARTICLE 12

GENERAL PROVISIONS

12.1 Relationship of the Parties. The Parties shall perform their obligations under this Amended and Restated Research Agreement as independent contractors and nothing contained in this Amended and Restated Research Agreement shall be construed to make either Codexis or Shell partners, joint venturers, principals, representatives or employees of the other. In particular, without limiting the generality of the foregoing, (a) none of the FTEs assigned by Codexis to perform its obligations under the Program shall be construed, or deemed to be, employees of Shell, and (b) none of the personnel assigned by Shell to perform its obligations under the Program shall be construed, or deemed to be, employees of Codexis. Neither Party shall have any right, power or authority, express or implied, to bind the other. Shell and Codexis agree that this Amended and Restated Research Agreement shall not constitute a partnership for tax purposes. In the event, however, that this Amended and Restated Research Agreement were so construed, then Shell and Codexis agree to be excluded from the provisions of Subchapter K of the United States Internal Revenue Code of 1986, as amended.

12.2 Assignments. Except as expressly provided herein, neither this Amended and Restated Research Agreement nor any interest hereunder may be assigned, nor any other obligation delegated, by a Party without the prior written consent of the other Party; provided, however, that each Party shall have the right to assign this Amended and Restated Research Agreement without consent to an Affiliate of such Party or to any successor in interest to such Party by way of merger, consolidation or other business reorganization or the sale of all or substantially all of its assets and further provided that in the event the non-assigning Party believes, in its sole discretion, that the assignment is to a direct competitor of such non-assigning Party in the Field of Use, such non-assigning Party may immediately terminate this Amended and Restated Research Agreement. This Amended and Restated Research Agreement shall be binding upon successors and permitted assigns of the Parties. Any assignment not in accordance with this Section 12.2 will be null and void.

12.3 Further Actions. Each Party agrees to execute, acknowledge and deliver such further instruments and to do all such other acts as may be necessary or appropriate in order to carry out the express provisions of this Amended and Restated Research Agreement.

12.4 Force Majeure. Neither Party shall be liable to the other for failure or delay in the performance of any of its obligations under this Amended and Restated Research Agreement for the time and to the extent such failure or delay is caused by earthquake, riot, civil commotion, war, terrorist acts, strike, flood, or governmental acts or restriction that is beyond the control of the respective Party. The Party affected by such force majeure will provide the other Party with full particulars thereof as soon as it becomes aware of the same (including its best estimate of the likely extent and duration of the interference with its activities), and will use commercially reasonable efforts to overcome the difficulties created thereby and to resume performance of its obligations as soon as practicable. If the performance of any obligation under this Amended and Restated Research Agreement is delayed owing to a force majeure for any continuous period of more than ninety (90) days, either Party may terminate this Amended and Restated Research Agreement by giving to the other Party not less than ten (10) business days notice in writing. In the event of any force majeure event that delays the performance of either Party under this Amended and Reseated Research Agreement, the Term shall automatically be extended for the period of time that such performance is delayed. In the event of any force majeure event that delays Codexis’ performance under this Amended and Restated Research Agreement, Shell’s payment obligations pursuant to Section 3.3 shall be suspended for the duration of such delay. Notwithstanding anything to the contrary, the payment of money shall not be subject to this Section 12.4.

12.5 Captions. The captions to this Amended and Restated Research Agreement are for convenience only, and are to be of no force or effect in construing or interpreting any of the provisions of this Amended and Restated Research Agreement.

12.6 Governing Law. This Amended and Restated Research Agreement will be governed by and interpreted in accordance with the laws of the State of New York, applicable to contracts entered into and to be performed wholly within the State of New York, excluding conflict of laws principles.

12.7 Dispute Resolution; Jurisdiction and Venue. Any controversy or claim (“Dispute”), whether based on contract, tort, statute or other legal or equitable theory (including but not limited to any claim of fraud, misrepresentation or fraudulent inducement or any question of validity or effect of this Amended and Restated Research Agreement including this clause) arising out of or related to this Amended and Restated Research Agreement (including but not limited to any amendments, annexations, and extensions) or the breach thereof shall be settled by consultation between the Parties initiated by written notice of the Dispute to the other Party. In the event such consultation does not settle the Dispute within thirty (30) days after written notice of such Dispute, then the Dispute shall be settled by binding arbitration in accordance with the then current commercial arbitration rules of the American Arbitration Association and this provision. The arbitration shall be governed by the United States Arbitration Act, 9 U.S.C. §§ 1-16 (the “Act”) to the exclusion of any provision of state law inconsistent therewith or which would produce a different result. Judgment upon the award rendered by the arbitrator may be

entered by any court having jurisdiction. The arbitration shall be held in Chicago, Illinois. The Parties shall attempt in good faith to agree on a single neutral arbitrator with relevant industry experience to conduct the arbitration. If the Parties do not agree on a single neutral arbitrator within ten (10) days after receipt of an arbitration notice, each Party shall select one (1) arbitrator and the two (2) Party-selected arbitrators shall select a third arbitrator with relevant industry experience to constitute a panel of three (3) arbitrators to conduct the arbitration in accordance with the Act. In the event that only one of the Parties selects an arbitrator, then such arbitrator shall be entitled to act as the sole arbitrator to resolve the Dispute or any and all unresolved issues subject to the arbitration. Each and all arbitrator(s) of the arbitration panel conducting the arbitration must and shall agree to render an opinion within twenty (20) days after the final hearing before the panel. The arbitrator(s) shall determine the claim of the Parties and render a final award in accordance with the substantive law of the State of New York, excluding the conflicts provisions of such law. The arbitrator shall set forth the reasons for the award in writing. The terms hereof shall not limit any obligations of a Party to defend, indemnify or hold harmless another Party against court proceedings or other claims, losses damages or expenses. All proceedings and decisions of the arbitrator(s) shall be deemed Confidential Information of each of the Parties, and shall be subject to Article 6 hereof. Notwithstanding anything herein to the contrary, a Party may seek a temporary restraining order or a preliminary injunction from any court of competent jurisdiction in order to prevent immediate and irreparable injury, loss, or damage on a provisional basis, pending the decision of the arbitrator(s) on the ultimate merits of any Dispute. Each Party agrees that all Disputes arising under this Amended and Restated Research Agreement shall be brought only against the Parties of this Agreement, as applicable and neither Party shall name an Affiliate company, except as may be required by Article 12.2.

12.8 Notices and Deliveries. Any notice, request, delivery, approval or consent required or permitted to be given under this Amended and Restated Research Agreement will be in writing and will be deemed to have been sufficiently given on the date of receipt if delivered in person, transmitted by telecopier (receipt verified) or by express courier service (signature required) or five (5) days after it was sent by registered letter, return receipt requested (or its equivalent), provided that no postal strike or other disruption is then in effect or comes into effect within two (2) days after such mailing, to the Party to which it is directed at its address or facsimile number shown below or such other address or facsimile number as such Party will have last given by notice to the other Party.

If to Codexis, addressed to:

Codexis, Inc.

000 Xxxxxxxxx Xxxxx

Xxxxxxx Xxxx, XX 00000

Attention: Chief Executive Officer

Telephone: 000-000-0000

Fax: 000-000-0000

with a copy to:

Codexis, Inc.

000 Xxxxxxxxx Xxxxx

Xxxxxxx Xxxx, XX 00000

Attention: General Counsel

Telephone: 000-000-0000

Fax: 000-000-0000

If to Shell, addressed to:

Shell Oil Products (US)

000 Xxxxxxxxx Xxxxxx

Xxxxxxx, XX 00000

Attention: Fuel Development Program Manager—Americas

Telephone: 000-000-0000

Fax: 000-000-0000

with a copy to:

Shell Oil Company

Associate General Counsel, Intellectual Property Services

000 Xxxxxxxxx

Xxxxxxx, XX 00000

Fax: 000-000-0000

12.9 No Consequential Damages. EXCEPT PURSUANT TO ARTICLE 10 OR AS A RESULT OF ANY CONFIDENTIALITY AGREEMENT ENTERED INTO BETWEEN CODEXIS AND A SHELL EMPLOYEE IN ACCORDANCE WITH SECTION 2.5(b), IN NO EVENT WILL A PARTY OR ANY OF ITS RESPECTIVE AFFILIATES BE LIABLE TO THE OTHER PARTY OR ANY OF ITS AFFILIATES FOR SPECIAL, INDIRECT, CONSEQUENTIAL OR PUNITIVE DAMAGES, WHETHER IN CONTRACT, WARRANTY, TORT, NEGLIGENCE, STRICT LIABILITY OR OTHERWISE, INCLUDING BUT NOT LIMITED TO, LOSS OF PROFITS OR REVENUE, OR CLAIMS OF CUSTOMERS OF ANY OF THEM OR OTHER THIRD PARTIES FOR SUCH DAMAGES.

12.10 Waiver. A waiver by a Party of any of the terms and conditions of this Amended and Restated Research Agreement in any instance will not be deemed or construed to be a waiver of such term or condition for the future, or of any subsequent breach hereof. All rights, remedies, undertakings, obligations and agreements contained in this Amended and Restated Research Agreement will be cumulative and none of them will be in limitation of any other remedy, right, undertaking, obligation or agreement of either Party.

12.11 Severability. When possible, each provision of this Amended and Restated Research Agreement will be interpreted in such manner as to be effective and valid under applicable law, but if any provision of this Amended and Restated Research Agreement is held to

be prohibited by or invalid under applicable law, such provision will be ineffective but only to the extent of such prohibition or invalidity, without invalidating the remainder of such provision or of this Amended and Restated Research Agreement. The Parties will make a good faith effort to replace the invalid or unenforceable provision with a valid one which in its economic effect is most consistent with the invalid or unenforceable provision.

12.12 Counterparts. This Amended and Restated Research Agreement may be executed simultaneously in counterparts, any one of which need not contain the signature of more than one Party but both such counterparts taken together will constitute one and the same agreement.

12.13 Compliance with Laws. Each Party shall comply with all applicable statutes, laws, regulations, enactments, directives and ordinances and all injunctions, decisions, directives, judgments and orders of any governmental authority in effect at any time in connection with the performance of its obligations under this Amended and Restated Research Agreement.

12.14 Amendment. No amendment of any provision of this Amended and Restated Research Agreement shall be binding on a Party to this Amended and Restated Research Agreement unless consented to in writing and signed by such Party. Signatures and writings in an electronic form do not constitute or create a writing signed by a Party.

[Signature page follows]

IN WITNESS WHEREOF, the Parties have caused this Amended and Restated Research Agreement to be executed by their respective duly authorized officers as of the Execution Date, each copy of which will for all purposes be deemed to be an original.


CODEXIS, INC.

By:		/s/ Xxxx Xxxx
Name:		Xxxx Xxxx
Title:		President

EQUILON ENTERPRISES LLC DBA SHELL OIL PRODUCTS US

By:		/s/ Xxxxx X. Xxxxxx
Name:		Xxxxx X. Xxxxxx
Title:		President

[Signature Page to Amended and Restated Collaborative Research Agreement]

EXHIBIT 1.21

Research Plans

Schedule 1

Research Plan for First Contract Year

Summary

Key technoeconomic parameters for the [*] include:

(i)

yield of [*],

(ii)

enzyme load,

(iii)

cost of enzyme manufacture,

(iv)

equipment costs,

(v)

residence time of reaction, and

(vi)

energy usage.

Enzyme systems improved for activity in [*] process conditions can reduce enzyme load requirements, reduce residence time, and improve volumetric productivity of [*]. Therefore, the goal of the research program is to [*].

For this 12 month research plan, efforts will be focused on:

(i)

identifying and obtaining [*] genes and enzymes to assemble a baseline [*] system,

(ii)

identifying and obtaining suitable [*], and

(iii)

enabling and executing an evolution campaign directed at [*].

Development of an evolution-suitable system will include:

(i)

establishment of a genetic expression system, and

(ii)

development of screening and assay formats, in each case suitable for high-throughput catalyst production and analysis.

Implementation of the evolution campaign will consist of

(i)

generation of initial genetic diversity,

(ii)

library design,

(iii)

DNA shuffling and library construction, and

(iv)

implementation of the screening program to identify enzyme variants possessing improved properties.

The screening process may consist of a series of tiered assays, starting with high-throughput, simple screens, and gradually shifting to lower throughput, but more informationally oriented assays. Assay data and mutational analysis will be assessed, and desirable variants and/or mutations will be re-introduced into subsequent “rounds” of evolution and screening, until enzyme variants are identified that meet or exceed the desired performance criteria. Ultimately, improved enzyme variants will be assessed under [*] conditions, which may include a

determination of their activity in the presence of other enzymes in the cellulase system, and activity on (or in the presence of) [*]. It is anticipated that the evolution campaign may begin with [*]; as more [*] and [*] are developed in the program, these may be implemented in the [*] process. This approach would allow for the simultaneous execution of the evolution campaign with assay development.

Introduction

Enzymatic saccharification of cellulosics involves a mixture of enzymes that work together synergistically. Cellulases such as endo-ß-1,4-glucanase (EC 3.2.1.4), exo-cellobiohydrolase (EC 3.2.1.91), and ß-glucosidase (ß-D-glucosidic glucohydrolase; EC 3.2.1.21) are required. In this type of system, endoglucanase and cellobiohydrolase enzymes degrade cellulose to cellobiose, which is then cleaved to glucose by ß-glucosidase. For hemicellulosic biomass, additional enzymes are required to degrade carbohydrate polymers such as xylan, arabinoxylan, and others; such enzymes include various xylanase, debranching enzymes, and others.

The available literature suggests that improvements in the cellulase system may be achieved by improving the activity of the [*] component. [*] and [*] are inhibited by [*] ([*]); for example, commonly used cellulases are inhibited by [*]% at a low concentration ([*] g/l) of [*] ([*]). One reported solution to this has been to add [*], however this has not been viewed as cost-effective. A preferred solution would be to [*]. Therefore, this [*] is suggested as a [*] for this program. Several improvements in the [*] enzymes may be desired, such as:

(i)

Decreased product inhibition. Although [*] enzymes from nature vary in their sensitivity to [*] inhibition, most [*] are highly sensitive to [*] inhibition, thereby limiting enzyme activity and overall [*] rate [*].

(ii)

Increased substrate tolerance. While some [*] from nature have been described [*], most [*] are inhibited by [*], limiting the potential for the final [*] rates.

(iii)

Increased specific activity. Activity improvements with these enzymes have been demonstrated to result in increases in [*].

(iv)

Increased activity in process environment (thermoactivity, thermotolerance, pH etc). Ideally, all enzymes required for use in a given reaction will possess matching preferences for the environmental aspects of the reaction, such as pH and temperature activity optima. For example, most [*] and [*] enzymes possess an optimal [*] of ~[*], so possessing a [*] with optimal activity at this [*] is desirable. The saccharification reaction may benefit from the [*] (i.e. [*] giving a [*] reaction), so increased activity at still [*] may also be desired. Since saccharification reactions typically run for considerable periods of time ([*]), [*] is likely important. [*] have been reported (e.g. [*]) and will be [*] as [*]. Other process-relevant traits of interest may include alteration of [*], and alleviation of inhibition from [*].

(v)

Altered substrate specificities. Although [*] are known to be most active on [*], some possess activity on [*] with varying efficiencies on various [*] of substrates. For

example, the [*] cellobiose, cellotriose, cellotetraose, cellopentaose, and cellohexaose, with [*] of [*], respectively ([*]). Changing the substrate orientation towards [*] might be advantageous either to the [*] of the [*], or for the [*] for the ensuing [*], which have different preferences for the [*] and [*] of [*].

(vi)

Increased expression, secretion. [*], a commonly used organism for cellulose production, does not produce and secrete sufficient [*] (~[*]% of total secreted proteins) to drive commercial saccharification demands ([*]). [*] cellulase preparations, [*], are considered most often for commercial saccharification ([*]), and [*] of this enzyme has been shown to result in increased saccharification ([*]). These enzymes could be engineered for improved expression for a particular expression host. Most [*] remain [*] of the producing fungus ([*]), which impedes their utility in saccharification. This feature is common in fungi, likely due to an evolutionary advantage of [*] the [*] near the [*] to facilitate the rapid [*] of [*] produced. This evolutionary constraint can [*], [*] the secretion capability and leading to a [*].

While particular enzymes in nature may possess certain characteristics for industrial use, it is rare that a native enzyme would possess all the preferred traits. The range of activities and properties known for related (homologous) enzymes may give an indication of the “evolvability” for a particular trait, that is, they are permitted by the enzyme [*]. Codexis technology allows for desirable properties from different enzymes to be combined, and improved further. Importantly, multiple properties may be evolved at the same time; such multi-trait evolution has been demonstrated using Codexis technology in other programs.

In addition to technical considerations, selection of [*] as the [*] provides practical advantages to the program, such as allowing for rapid program implementation due to the [*] of the [*], and a good potential for rapid implementation of [*] such as [*] and [*]. Starting materials for this [*] are likely to be available, including [*]. [*] should be of use in the development of the cellulase system.

Other enzyme targets for improvement will be considered during the course of the program. Possible candidates might include [*]. In each case, it is suggested that [*] utilize [*], or at a minimum [*]. This would allow for progress in the evolution campaign whilst the [*] formats are developed.

Process Definition

At the initiation of the program, an extensive review of the scientific, commercial, and patent literature will be conducted. Due to the large amount of prior work in this area, this is anticipated to be a significant task. This review is required to establish a reasonable understanding of relevant technical issues and, importantly, the intellectual property landscape, and the validation of appropriate research targets and materials. Suitable starting enzymes and the genes that encode them will be identified for use in the program. Possible licensing opportunities with third parties may also be identified. This activity will continue throughout the life of the research program in order to stay abreast of new information released during the

program term.

Establishing a System for the [*] Evolution Campaign

Genetic System Development for [*]

Several [*] sources of [*] have been identified and functionally expressed/secreted in prokaryotic and eukaryotic hosts. The starting gene(s) that will be used in this program will be determined by the [*] and [*]. One particular benefit to [*] is that if the program is [*], the program may be [*], even one with [*]. Codexis has successfully employed this approach in many other programs. Other relevant information, such as [*], will be analyzed.

Genes will be obtained [*], and their expression in appropriate [*] hosts will be assessed. High-throughput growth and expression formats will be developed to enable the handling of, for example, [*] isolates [*]. Suitable screening formats will result in the detection of the appropriate enzymatic activity in high-throughput, utilizing assay methods also developed under the program.

Assay Development [*]

[*]. If a genetic selection or a visual +/- activity screen utilizing is possible, very large numbers of isolates [*] may be screened to enrich for live isolates and exclude inactive isolates. Such selections and assays are possible for this target, and these will be tested for utility in this program. For example, a shuffled library expressed in a host strain (without [*] activity) may be plated on agar containing [*]; only isolates possessing active enzyme would survive. Alternatively, a colorimetric substrate or assay may be available, allowing for rapid visual identification of active isolates. These techniques are particularly useful when libraries [*]. More analytical methods for the isolation/extraction, separation, and detection of relevant compounds (such as [*]) will be developed and implemented. At least one analytical method should be suitable for use in sufficient throughput (e.g. [*]) to enable characterization of shuffled libraries, even in the absence of a prescreen or selection. The screening process will continue through more refined and more information-rich assays in lower throughput until the desired understanding of activity is obtained.

Appropriate characteristics for the desired enzyme activity will be incorporated into the assay, [*].

Ultimately, more complex assays will be used for screening. For example, assays incorporating [*], and/or a [*] enzyme system, are important to the confirmation of the desired activity. However, such complex assays and systems require development. Therefore, the initial screening will proceed with [*] (e.g. [*] and [*]); the complex assays will be developed in parallel until they are sufficiently developed for use in the screening program. The enablement of [*] for [*] for assay is a significantly [*]. This will include accurate [*] of [*], and [*] amenable implementation of [*] throughout the assay and [*] process. [*] (available commercially) and [*] are included in this format. External sources of [*] will need to be

identified and secured during the course of the program. Such sources might include [*], [*] and/or [*]. [*] may contain significant amounts of other [*], and will likely present additional [*] and assay.

[*].

The development of such [*] assays enables the assessment of [*] in systems, as well as supporting the future screening needs for the evolution of additional [*] enzymes, [*].

Evolution Campaign [*]

[*]. Once sufficient genetic diversity is in hand, shuffled libraries will be generated to recombine mutations. Family shuffling, a technique that can recombine related genes (e.g. from different organisms) may also be used to exchange large blocks of genetic sequences. As such libraries are created and screened, the relationships between sequences and activities are assessed using a proprietary statistical method (ProSAR). Beneficial mutations and potentially beneficial mutations are carried through into subsequent library designs and rescreened, while deleterious mutations are discarded. Subsequent libraries may also include error-prone methods should additional diversity be desired in the library. This process of analysis, design, library construction and screening may be repeated many times to achieve desired activities.

It is anticipated that at least [*] rounds of shuffling and screening may be completed for this [*] within the 12 month period.

Establishing a Benchmark [*] System

The [*] improvement program entails [*], which can then be used to assess shuffled [*] for improved properties. There are several different paths to enable this analysis. A preferred approach would entail cloning of the necessary [*] genes, production of enzymes separately, and formulation of the [*]. This approach would require functional expression of each of the [*] enzymes, and production of sufficient quantities of each enzyme for the activity studies. Using this approach, evolved enzyme variants may be substituted for unevolved enzymes (e.g. from the “baseline” system), and activities may be compared. Since this format allows for the independent control of each enzyme’s loading, a factorial optimization of the [*] mixture is possible, [*].

There are other approaches to enable a benchmark [*] system for the analysis of evolved enzyme variants. Although these are less desirable than that described above, they may be used as alternatives should difficulties arise. For example, it may be possible to obtain pure enzymes for each of the components from [*], and proceed as above. A challenge to using this approach is that commercial [*] preparations tend to contain mixtures of [*], making deconvolution of the activities difficult.

Alternatively, a [*] mixture such as that produced by a [*] producing organism (e.g. [*]) may be used as a baseline cocktail. The evolved enzyme could be spiked into the mixture, and activity compared to that obtained using the unevolved (parent) enzyme. This approach is similar to some commercial processes in which the activity of the system is “topped up” by the

addition of separately made enzymes. However, while this approach may be easier and quicker to achieve, the mixture of enzymes is neither controllable nor quantifiable, so the information derived from the experiment will like be of less value than that obtained by the preferred method above.

Another alternative would be to produce the [*] enzymes from [*]. This would provide stoichiometric control at the level, and perhaps assumed control of enzyme concentrations, although it would not enable independent control of each enzyme’s concentration. This may also enable [*].

EXHIBIT 1.32

Year One Final Milestone

The Year One Final Milestone will consist of achievement of the [*] Performance Criteria and the Model [*] System Criteria set forth below:

[*] Performance Criteria:

A starting [*] enzyme will be evolved for improved activity using [*] substrate. Performance of the evolved [*] must show at least a [*] improvement compared to the performance of the starting [*] as measured by [*] under reaction conditions to include:

•

[*] g/L substrate [*]

•

[*] g/L [*]

•

[*] buffer, [*]

•

24 h, [*] ^o C

Model [*] System Criteria:

Put in place a model [*] system [*] will enable the evaluation of [*].

EXHIBIT 2.8(E)(II)

Form Sponsored Research Agreement

SPONSORED RESEARCH AGREEMENT

THIS SPONSORED RESEARCH AGREEMENT (“Agreement”), is made as of the day of , 200 (the “Effective Date”), by and between CODEXIS, INC., with principal place of business at 000 Xxxxxxxxx Xxxxx, Xxxxxxx Xxxx, Xxxxxxxxxx 00000 XXX (“Codexis”), and , with a principal place of business at (“Company”).

In consideration of the mutual agreement between the parties hereto, it is agreed as follows:

Section 1. PRINCIPAL INVESTIGATOR AND RESEARCH PLAN

(a) Company will undertake the research project entitled “ ” (“Study”), in accordance with the research plan attached hereto as Exhibit A (the “Research Plan”), under the direction of (the “Principal Investigator”). Any change in the scope of work to be performed with respect to the Study requires Codexis’ prior written approval. The work will be commenced on , 200_ and will be completed within five (5) days thereafter.

(b) Company represents and warrants that it is in possession of all necessary equipment to accomplish the Study, including the specific equipment listed in Section of the Research Plan (the “will be due and payable in accordance with Section 3.6 only after the achievement of”) and it will utilize such Necessary Equipment in the conduct of the Study.

(c) Company and Principal Investigator agree that all work for the Study will be performed at Company’s facility located at (“Facility”). Company and Principal Investigator agree that a single representative of Codexis (the “Codexis Representative”) and a single representative (the “Shell Representative”) of Equilon Enterprises LLC dba Shell Oil Products US (“Shell”) shall be present at all times during the conduct of the Study at the Facility, which shall be scheduled at the mutual convenience of the Principal Investigator, the Codexis Representative and the Shell Representative.

Section 2. CODEXIS ENZYMES.

(a) Codexis will provide Principal Investigator with sufficient amounts of its [proprietary enzymes or microbes] identified on Exhibit B hereto (the “Codexis Enzymes”) to conduct the Study as provided in the Research Plan. Company and Principal Investigator agree

to use the Codexis Enzymes in strict accordance with the Research Plan, and not for any other purpose. Company and Principal Investigator shall not attempt to reverse engineer, deconstruct, in any way determine the structure or composition of any of the Codexis Enzymes, or modify the Codexis Enzymes in any way. Codexis Enzymes will not be used in humans under any circumstances, and will not be transferred to others outside of Principal Investigator’s laboratory except with Codexis’ prior written approval. Upon termination or expiration of the Study, Company and Principal Investigator will return any and all remaining quantities of Codexis Enzymes to Codexis.

(b) Company and Principal Investigator understand and agree that the Codexis Enzymes are experimental in nature and should be used with caution and prudence since all of their characteristics are not known. THE CODEXIS ENZYMES ARE SUPPLIED WITH NO WARRANTIES OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.

(c) Company and Principal Investigator acknowledge and agree that the Codexis Enzymes are and shall remain the sole property of Codexis.

(d) Company and Principal Investigator agree, to the extent permitted by governing law, to hold Codexis harmless from any claims or liability resulting from use of the Codexis Enzymes, except insofar as such claims or liability arise out of the gross negligence or wrongdoing of Codexis.

Section 3. PAYMENT

The total cost to Codexis for the work under this Agreement (inclusive of direct and indirect costs) is Dollars (US$ .00) to be paid to Company as follows: [FILL IN SPECIFIC PAYMENT TERMS; WHAT FOLLOWS IS A SAMPLE APRPOACH] (a) Dollars (US$ .00) promptly after signing of this Agreement by each of the parties and the Principal Investigator, and receipt by Codexis (attn: Accounts Payable) of an invoice requesting such payment; and (b) Dollars (US$ .00) promptly after receipt by Codexis (attn: ) of a satisfactory final report for the Study (as set forth in Section 4) and receipt by Codexis (attn: Accounts Payable) of an invoice requesting such payment. Each check shall include the title of the Study and the name of the Company and the Principal Investigator.

Section 4. REPORT

(a) Principal Investigator will provide a written report to Codexis (to the attention of ) regarding the work performed under the Research Plan, such report to be due no later than two (2) weeks after such work is completed. All reports shall be considered Confidential Information of Codexis (as defined below), and shall not be provided or disclosed to any party other than Codexis, except that a single copy of the report shall also be sent to Shell at the following address: .

Section 5. TERM OF AGREEMENT AND TERMINATION

(a) This Agreement shall be in effect from the Effective Date through , 200 , unless earlier terminated as provided herein. The parties may extend the term of this Agreement by mutual written agreement.

(b) Either party may terminate this Agreement, such termination to be effective upon thirty (30) days’ prior written notice to the other party, for any reason. If such termination is by Company, it shall refund any unused funding promptly to Codexis.

(c) If the Principal Investigator leaves the Company or is unable or unwilling to perform the Services required under this Agreement, Codexis may terminate this Agreement, with such termination to be effective thirty (30) days after written notice to the Company. The Company shall refund any unused funding promptly to Codexis.

(d) If Codexis terminates this Agreement pursuant to Section 5(c), Codexis will reimburse Company for all noncancellable obligations and expenses incurred through the date of termination. The provisions of Sections 2(b), 2(c), 2(d), 6, 7, 8, 10 and this Section 5(d) will survive expiration or termination of this Agreement.

Section 6. CONFIDENTIALITY

(a) Company and Principal Investigator agree to maintain in confidence and not to disclose or transfer to any other party the following: the existence and terms and conditions of this Sponsored Research Agreement; the Research Plan; all data and results of the work under this Agreement; all know-how, practices, processes, patentable and non-patentable inventions arising from the work under this Agreement; and all other information disclosed by Codexis to Company or Principal Investigator under this Agreement, whether in written, oral, graphic or electronic form (collectively referred to as “Confidential Information”). Company and Principal Investigator will use the Confidential Information only for purposes of conducting the Study and for no other purpose. Notwithstanding the foregoing, Company may disclose the Confidential Information to those of its employees who need to know such Confidential Information to perform its obligations under this Agreement, provided that such employees agree in writing to be bound by the terms of this Agreement.

(b) Disclosure of Confidential Information shall not be precluded if such disclosure is required under court order or applicable law or regulation, provided that Company first gives written notice to Codexis of the need for such disclosure so that Codexis may seek a protective order or other confidential treatment (if available).

(c) Upon termination or expiration of the Study, Company and Principal Investigator will return any and all Confidential Information to Codexis, except that Principal Investigator may retain one (1) copy solely for archival purposes.

(d) Notwithstanding anything to the contrary, Company and Principal

Investigator may disclose (i) Confidential Information to the Shell Representative during the conduct of the Study, and (ii) the written report to Shell pursuant to Section 4(a).

(e) Without limiting the generality of the foregoing, Company and Principal Investigator acknowledge and agree that Confidential Information may not be published or disclosed in any scientific or other publication and this Section 6 precludes any such scientific or other publication or disclosure of any Confidential Information.

Section 7. PATENTS AND INVENTIONS

(a) At no additional cost, Company and Principal Investigator hereby assign to Codexis title to all know-how, all patentable and non-patentable inventions, and all other proprietary technology arising from the work under this Agreement or resulting from use of the Codexis Enzymes. Company warrants that each Company employee and other persons, if any, performing work under this Agreement is under obligation to assign all rights in any know-how, all patentable and non-patentable inventions, and all other proprietary technology resulting from the use of the Codexis Enzymes to Company. Codexis is free to use for any purposes information or materials supplied to it under this Agreement, and shall have the option (but not the obligation) to file at its own expense patent applications describing and claiming inventions it believes to be patentable. Company and Principal Investigator agree to cooperate, at Codexis’ expense, in filing such applications (if any) and in the prosecution and maintenance of them before patent offices.

(b) No right or license is granted to Company or Principal Investigator with respect to the Codexis Enzymes, either expressly or by implication, other than the right to use the same for the work under the Research Plan in accordance with this Agreement.

Section 8. USE OF NAME

Company and Principal Investigator agree not to use Codexis’ name without prior consent, except as necessary to identify Company as the Study site and Principal Investigator when required or desired to do so.

Section 9. NOTICES

Any notice to be given pursuant to this Agreement must be in writing and sent by telecopy or by overnight courier to the addresses set forth below. Notice shall be deemed to have been received on the same business day as telecopy (with machine confirmation of receipt) or three (3) business days following delivery of the document(s) to the courier.


		If to Company:		If to Codexis
				Codexis, Inc.
				Attn: General Counsel
				000 Xxxxxxxxx Xxxxx
				Xxxxxxx Xxxx, Xxxxxxxxxx 00000
				Telecopy: x0 (000) 000-0000


		With a copy to:


		Telecopy:

Section 10. ASSIGNMENT

This Agreement shall not be assigned or otherwise transferred by Company or Principal Investigator to any party without Codexis’ prior written consent.

Section 11. MISCELLANEOUS

(a) This Agreement, including Exhibits A and B, contains the entire agreement of the parties on the subject matter to which it relates, and supersedes all prior and contemporaneous proposals, discussions, and writings, by and between the parties, on such subject. No commitment or modification hereof shall be valid or binding upon the parties unless made in writing and signed by authorized representatives of the parties. No delay or omission by any party in exercising any right hereunder, at law or in equity, or any otherwise, shall impair any such right, or be construed as a waiver thereof, or any acquiescence therein, nor shall any single or partial exercise of any right preclude other or further exercise thereof, or the exercise of any other right. This Agreement shall be governed by the laws of , without regard to its conflict of laws principles.

(b) Company and Principal Investigator represent to Codexis that the terms of this Agreement do not violate and will not cause a breach of the terms of any other agreement or, to Company or Principal Investigator’s knowledge, any applicable law, decree or regulations, to which Company or Principal Investigator is a party or by which it is subject or bound. Company and Principal Investigator further covenant that Company and Principal Investigator will not enter into any third party agreement where the terms of this Agreement will violate or cause a breach of the terms of such third party agreement.

(c) This Agreement may be executed in counterparts, each of which shall be treated as an original, but which together shall constitute a single instrument.

(d) No Third Party Beneficiaries. The parties to this Agreement do not intend that any terms hereof should be enforceable by any person who is not a party to this Agreement.

IN WITNESS WHEREOF, a duly authorized representative of each party has executed this Agreement as of the Effective Date set forth above.


CODEXIS, INC.		[COMPANY]


By:						By:

Name:						Name:

Its:						Its:

I am the Principal Investigator for the Study described in this Agreement. By signing below, I indicate that I have reviewed this Agreement prior to committing to undertake the Study and agree to comply with the terms and conditions of this Agreement.


Principal Investigator Signature:



		Name:

SCHEDULE A

Series D Stock Purchase Agreement

CODEXIS, INC.

SERIES D PREFERRED STOCK PURCHASE AGREEMENT

August 22, 2006

TABLE OF CONTENTS


			Page
1.	Agreement to Sell and Purchase		1

	1.1	Authorization of Shares	1

	1.2	Sale and Purchase	1

2.	Closing, Delivery and Payment		1

	2.1	Closing	1

	2.2	Subsequent Closings	2

	2.3	Delivery	2

3.	Representations and Warranties of the Company		2

	3.1	Organization, Good Standing and Qualification	3

	3.2	Subsidiaries	3

	3.3	Capitalization; Voting Rights	3

	3.4	Authorization; Binding Obligations	5

	3.5	Financial Statements	5

	3.6	Liabilities	5

	3.7	Agreements; Action	5

	3.8	Obligations to Related Parties	6

	3.9	Changes	7

	3.10	Title to Properties and Assets; Liens, Etc.	8

	3.11	Intellectual Property	8

	3.12	Compliance with Other Instruments	9

	3.13	Litigation	10

	3.14	Taxes	10

	3.15	Employees	11

	3.16	Registration Rights and Voting Rights	11

	3.17	Compliance with Laws; Permits	11

	3.18	Environmental and Safety Laws	12

	3.19	Offering Valid	13

	3.20	Full Disclosure	13

	3.21	Minute Books	13

	3.22	Real Property Holding Corporation	13

	3.23	Executive Officers and Directors	13



	3.24	Insurance	14

	3.25	Regulatory Compliance	14

4.	Representations and Warranties of the Purchasers		14

	4.1	Requisite Power and Authority	14

	4.2	Investment Representations	15

	4.3	Transfer Restrictions	16

5.	Conditions to Closing		16

	5.1	Conditions to the Purchasers’ Obligations at the Closing	16

	5.2	Conditions to the Company’s Obligations at the Closing	17

6.	Miscellaneous		18

	6.1	Governing Law	18

	6.2	Survival	18

	6.3	Successors and Assigns	18

	6.4	Entire Agreement	19

	6.5	Severability	19

	6.6	Amendment and Waiver	19

	6.7	Delays or Omissions	19

	6.8	Notices	19

	6.9	Expenses	19

	6.10	Attorneys’ Fees	20

	6.11	Titles and Subtitles	20

	6.12	Counterparts	20

	6.13	Broker’s Fees	20

	6.14	Pronouns	20

	6.15	California Corporate Securities Law	20


EXHIBITS

Exhibit A		Schedule of Purchasers
Exhibit B		Fifth Amended and Restated Certificate of Incorporation
Exhibit C		Third Amended and Restated Investor Rights Agreement
Exhibit D		Second Amended and Restated Right of First Refusal and Co-Sale Agreement
Exhibit E		Third Amended and Restated Voting Agreement
Exhibit F		Form of Opinion of Xxxxxx & Xxxxxxx LLP

CODEXIS, INC.

SERIES D PREFERRED STOCK PURCHASE AGREEMENT

This Series D Preferred Stock Purchase Agreement (the “Agreement”) is made and entered into as of August 22, 2006, by and among Codexis, Inc., a Delaware corporation (the “Company”), and the purchasers, severally and not jointly, listed on Exhibit A hereto, each of which is herein referred to as a “Purchaser” and all of which are collectively referred to herein as the “Purchasers”.

Recitals

WHEREAS, the Company has authorized the sale and issuance of up to an aggregate of ten million one hundred thousand seven hundred and fifty six (10,100,756) shares of its Series D Preferred Stock (the “Shares”); and

WHEREAS, the Company desires to issue and sell the Shares to the Purchasers upon the terms and subject to the conditions set forth herein.

Agreement

NOW, THEREFORE, in consideration of the foregoing recitals and the mutual promises, representations, warranties, and covenants hereinafter set forth and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree as follows:

1. Agreement to Sell and Purchase.

1.1 Authorization of Shares. On or prior to the Initial Closing (as defined in Section 2.1 below), the Company shall have authorized (a) the sale and issuance to the Purchasers of the Shares and (b) the issuance of such shares of Common Stock to be issued upon conversion of the Shares (the “Conversion Shares”). The Shares and the Conversion Shares shall have the rights, preferences, privileges and restrictions set forth in the Fifth Amended and Restated Certificate of Incorporation of the Company, in the form attached hereto as Exhibit B (the “Restated Charter”), which shall have been adopted by the Company and filed with the Secretary of State of the State of Delaware on or before the Initial Closing.

1.2 Sale and Purchase. Upon the terms and subject to the conditions hereof, at each Closing the Company hereby agrees to issue and sell to each Purchaser, and each Purchaser agrees to purchase from the Company, that number of Shares set forth opposite each Purchaser’s name on Exhibit A hereto, at a purchase price of three dollars and ninety seven cents ($3.97) per share.

2. Closing, Delivery and Payment.

2.1 Closing. The initial closing of the sale and purchase of the Shares under this Agreement (the “Initial Closing”) shall take place at 11:00 a.m., at the offices of Xxxxxx &

Xxxxxxx LLP, 000 Xxxxx Xxxxx, Xxxxx Xxxx, XX 00000 on such date as the Company and the Purchasers acquiring in the aggregate more than half of the Shares shall mutually agree, or at such other time, date and place as the Company and the Purchasers acquiring in the aggregate more than half of the Shares shall mutually agree (such date is hereinafter referred to as the “Initial Closing Date”).

2.2 Subsequent Closings. Subject to the terms and conditions of this Agreement, the Company may sell, on or before October 22, 2006, any unsold Shares (up to a maximum aggregate of ten million one hundred thousand seven hundred and fifty six (10,100,756) shares at all Closings (as defined below), at the same price per share as the Shares sold at the Initial Closing to such other persons and entities as are determined by the Company and the Board of Directors of the Company, and approved in writing by holders of sixty percent (60%) of the Common Stock issuable or issued upon the conversion of the Shares (each approved new investor, an “Additional Purchaser”), following the fulfillment or waiver of the conditions set forth in Section 5 hereof or at such other time and place as the Company and the Additional Purchaser(s) mutually agree upon, orally or in writing (each of which time and place is designated as a “Subsequent Closing,” and with the Initial Closing, each a “Closing”). Any Additional Purchaser shall be considered a “Purchaser” for purposes of this Agreement, and any Series D Preferred Stock so acquired by such Additional Purchaser shall be considered “Shares” for the purposes of this Agreement and all other agreements contemplated hereby upon execution by such Additional Purchaser of an appropriate counterpart signature page. Upon each such event, the Company shall prepare and distribute to the Purchasers (including the Additional Purchasers) a revised Exhibit A, which shall include the name of each Additional Purchaser and the number of shares of Series D Preferred Stock to be purchased by each Additional Purchaser. Upon the Subsequent Closing of the sale of shares of Series D Preferred Stock to any Additional Purchaser, such Additional Purchaser shall also, as evidenced by an applicable executed counterpart signature page, become a party to the Related Agreements and shall have the rights and obligations hereunder and thereunder. Each Subsequent Closing shall take place at the offices of Xxxxxx & Xxxxxxx LLP, 000 Xxxxx Xxxxx, Xxxxx Xxxx, Xxxxxxxxxx. The Purchasers hereby irrevocably waive any pre-emptive rights or rights of first offer, and related notice rights, they may possess now or hereafter with respect to sales of Series D Preferred Stock made pursuant to this Section 2.2.

2.3 Delivery. At each Closing, upon the terms and subject to the conditions hereof, the Company will deliver to each Purchaser a certificate or certificates representing that number of Shares set forth opposite such Purchaser’s name on Exhibit A hereto against payment of the purchase price therefore by check, wire transfer, cancellation of indebtedness (plus any accrued interest thereon) or any combination of the foregoing, at the option of each Purchaser. If a Purchaser effects payment in whole or in part by cancellation of indebtedness, then such Purchaser shall surrender to the Company for cancellation at the applicable Closing any evidence of such indebtedness or shall execute an instrument of cancellation in form and substance acceptable to the Company.

3. Representations and Warranties of the Company. Except as set forth on a Schedule of Exceptions delivered by the Company to the Purchasers, the Company hereby represents and warrants to the Purchasers as of the date of this Agreement and as of the Initial Closing as set forth below.

3.1 Organization, Good Standing and Qualification. The Company is a corporation duly organized, validly existing and in good standing under the laws of the State of Delaware. The Company has all requisite corporate power and authority: (i) to own and operate its properties and assets, (ii) to execute and deliver this Agreement, the Third Amended and Restated Investor Rights Agreement in the form attached hereto as Exhibit C (the “Investor Rights Agreement”), the Second Amended and Restated Right of First Refusal and Co-Sale Agreement in the form attached hereto as Exhibit D (the “Co-Sale Agreement”) and the Third Amended and Restated Voting Agreement in the form attached hereto as Exhibit E (the “Voting Agreement”) (collectively, the “Related Agreements”), (iii) to issue and sell the Shares and the Conversion Shares, (iv) to carry out the provisions of this Agreement, the Related Agreements and the Restated Charter and (v) to carry on its business as presently conducted and as proposed to be conducted. The Company is duly qualified and is authorized to do business and is in good standing as a foreign corporation in all jurisdictions in which the nature of its activities and of its properties (both owned and leased) makes such qualification necessary, except for those jurisdictions in which failure to do so would not have a material adverse effect on the Company or its business.

3.2 Subsidiaries. The Company does not own or control any equity security or other interest of any other corporation, limited partnership or other business entity. The Company is not a participant in any joint venture, partnership or similar arrangement.

3.3 Capitalization; Voting Rights.

(a) The authorized capital stock of the Company, immediately prior to the Initial Closing, consists of (i) forty million (40,000,000) shares of Common Stock, par value $0.0001 per share, of which one million, seven hundred twenty-four thousand, one hundred sixty six (1,724,166) shares are issued and outstanding, and (ii) twenty-six million six hundred fifteen thousand seven hundred forty-six (26,615,746) shares of Preferred Stock, par value $0.0001 per share, six million (6,0000,000) of which are designated Series A Preferred Stock, all of which are issued and outstanding, eight million one hundred one thousand one hundred one (8,101,101) of which are designated Series B Preferred Stock, all of which are issued and outstanding, one million five hundred fourteen thousand six hundred forty-five (1,514,645) of which are designated Series C Preferred Stock, all of which are issued and outstanding, and eleven million (11,000,000) of which are designated Series D Preferred Stock, none of which are issued and outstanding. The Company has a right of first refusal over transfers of all outstanding shares of Common Stock.

(b) The Company has reserved 9,100,000 shares of Common Stock for issuance to officers, directors, employees and consultants of the Company pursuant to its 2002 Stock Plan duly adopted by the Board of Directors and approved by the Company’s stockholders (the “Stock Plan”). Of such reserved shares of Common Stock, 375,177 shares have been issued pursuant to exercised options, options to purchase 4,788,792 shares have been granted and are currently outstanding and 3,395,031 shares of Common Stock remain available for issuance pursuant to future grants under the Stock Plan. The Company has reserved (i) an aggregate of 46,176 shares of Common Stock for issuance to Lighthouse Capital Partners IV, L.P. and Lighthouse Capital Partners IV, L.P. pursuant to warrants dated February 12, 2004 (the “Lighthouse Warrants”), (ii) an aggregate maximum of 65,000 shares of Common Stock

pursuant to the Non-Qualified Stock Option Agreement dated as of February 23, 2004 and Non-Qualified Stock Option Agreement dated as of January 1, 2005, each by and between the Company and Xxxxxx & Xxxxxxx LLP (the “Xxxxxx Options”), (iii) 9,100 shares of Common Stock for issuance to Oxford Finance Corporation pursuant to a warrant dated October 25, 2005 (the “Oxford Warrant”) and (iv) an aggregate of 323,568 shares of Series D Preferred Stock for issuance to certain investors of the Company pursuant to warrants dated May 25, 2006 (the “Bridge Warrants”). At the Initial Closing, except for (i) outstanding options issued pursuant to the Stock Plan, the Lighthouse Warrants, the Xxxxxx Options, the Oxford Warrant and the Bridge Warrants and as set forth on Section 3.3(b) of the Schedule of Exceptions or options that may be issued in the ordinary course of business after August 22, 2006, (ii) the conversion privileges of the Preferred Stock and (iii) the rights granted pursuant to this Agreement and the Related Agreements, there are no outstanding options, warrants, rights (including conversion or preemptive rights and rights of first refusal), proxy or stockholder agreements, or agreements of any kind for the purchase or acquisition from the Company of any of its securities.

(c) All issued and outstanding shares of the Company’s Common Stock and Preferred Stock (i) have been duly authorized and validly issued and are fully paid and nonassessable and (ii) were issued in compliance with all applicable state and federal laws concerning the issuance of securities.

(d) At the Initial Closing, the rights, preferences, privileges and restrictions of the Shares are as stated in the Restated Charter. Each series of Preferred Stock is convertible into Common Stock on a one-for-one basis as of the date hereof and the consummation of the transactions contemplated hereunder will not result in any anti-dilution adjustment or other similar adjustment to the outstanding shares of Preferred Stock. The Conversion Shares have been duly and validly reserved for issuance. When issued in compliance with the provisions of this Agreement and the Restated Charter, the Shares and the Conversion Shares will be validly issued, fully paid and nonassessable and will be free of any liens or encumbrances other than liens and encumbrances created by or imposed upon the Purchaser by entities other than the Company; provided, however, that the Shares and the Conversion Shares may be subject to restrictions on transfer under state and/or federal securities laws as set forth herein or as otherwise required by such laws at the time a transfer is proposed.

(e) All outstanding securities of the Company, including, without limitation, all outstanding shares of the capital stock of the Company, all shares of the capital stock of the Company issuable upon the conversion or exercise of all convertible or exercisable securities and all other securities that the Company is obligated to issue, are subject to a one hundred eighty (180) day “market stand-off” restriction upon an initial public offering of the Company’s securities pursuant to a registration statement filed with the Securities and Exchange Commission (“SEC”) pursuant to the Securities Act of 1933, as amended (the “Securities Act”) in a form substantially identical to Section 2.12 of the Investor Rights Agreement.

(f) No stock plan, stock purchase, stock option or other agreement or understanding between the Company and any holder of any securities or rights exercisable or convertible for securities provides for acceleration or other changes in the vesting provisions or other terms of such agreement or understanding as the result of the occurrence of any event.

3.4 Authorization; Binding Obligations. All corporate action on the part of the Company, its officers, directors and stockholders necessary for the authorization of this Agreement and the Related Agreements, the performance of all obligations of the Company hereunder and thereunder at the Initial Closing and the authorization, sale, issuance and delivery of the Shares pursuant hereto and the Conversion Shares pursuant to the Restated Charter has been taken or will be taken prior to the Initial Closing. The Agreement and the Related Agreements, when executed and delivered, will be valid and binding obligations of the Company enforceable in accordance with their terms, except (a) as limited by applicable bankruptcy, insolvency, reorganization, moratorium or other laws of general application affecting enforcement of creditors’ rights, (b) general principles of equity that restrict the availability of equitable remedies, and (c) to the extent that the enforceability of the indemnification provisions may be limited by applicable laws. The issuance of the Shares hereunder and the subsequent conversion of the Shares into Conversion Shares are not and will not be subject to any preemptive rights or rights of first refusal that have not been properly waived or complied with.

3.5 Financial Statements. The Company has provided to the Purchasers (a) its financial statements (balance sheet and income and cash flow statements) at December 31, 2004, (b) its unaudited financial statements (balance sheet and income and cash flow statements) at December 31, 2005 and (c) its unaudited financial statements balance sheet and income and cash flow statements) as, at and for the six-month period ended June 30, 2006 (the “Statement Date”) (collectively, the “Financial Statements”). The Financial Statements, together with the notes thereto, are complete and correct in all material respects and have been prepared in accordance with generally accepted accounting principles in the United States (“GAAP”) consistently applied and present fairly the financial condition and position of the Company as of their respective dates; provided, however, that the unaudited Financial Statements are subject to normal recurring year-end audit adjustments (which will not be material either individually or in the aggregate), and do not contain all footnotes required under GAAP.

3.6 Liabilities. The Company has no material liabilities and no material contingent liabilities that are not disclosed in the Financial Statements, except (i) current liabilities incurred in the ordinary course of business subsequent to the Statement Date that have not been, either in any individual case or in the aggregate, materially adverse to the financial condition or operating results of the Company and (ii) obligations under contracts and commitments incurred in the ordinary course of business and not required under GAAP to be reflected in the Financial Statements, which, in both cases, individually or in the aggregate, are not material to the financial condition or operating results of the Company. The Company is not a guarantor or indemnitor of any indebtedness of any third party.

3.7 Agreements; Action.

(a) Except for the Related Agreements there are no agreements, understandings or proposed transactions between the Company and any of its officers, directors, affiliates or any affiliate thereof.

it is bound, that may involve (i) obligations (contingent or otherwise) of, or payments to, the Company in excess of $50,000, or (ii) the transfer or license of any patent, copyright, trade secret or other proprietary right to or from the Company (other than licenses arising from the purchase of “off the shelf” or other standard products), (iii) indemnification by the Company with respect to infringements of proprietary rights (other than indemnification obligations arising from purchase or license agreements entered into in the ordinary course of business), (iv) provisions restricting or affecting development, manufacture, or distribution of the Company’s products or services or proposed products or services or (v) any other material agreement.

(c) The Company has not (i) declared or paid any dividends, or authorized or made any distribution upon or with respect to any class or series of its capital stock, (ii) incurred or guaranteed any indebtedness for money borrowed or any other liabilities individually in excess of $50,000 or, in the case of indebtedness and/or liabilities individually less than $50,000, in excess of $250,000 in the aggregate, (iii) made any loans or advances to any person, other than ordinary advances for travel expenses, or (iv) sold, exchanged or otherwise disposed of any of its assets or rights, other than the sale of its inventory in the ordinary course of business.

(d) For the purposes of subsections (b) and (c) above, all indebtedness, liabilities, agreements, understandings, instruments, contracts and proposed transactions involving the same person or entity (including persons or entities the Company has reason to believe are affiliated therewith) shall be aggregated for the purpose of meeting the individual minimum dollar amounts of such subsections.

(e) The Company is not a party to and is not bound by any contract, agreement or instrument that materially adversely affects its business as now conducted or as proposed to be conducted, its properties or its financial condition.

(f) The Company has not engaged in the past three months in any discussion (i) with any representative of any corporation or corporations whereby the Company has agreed to or plans to consolidate or merge the Company with or into any such corporation or corporations, (ii) with any corporation, partnership, association or other business entity or any individual whereby the Company has agreed to or plans to sell, convey or dispose of all or substantially all of the assets of the Company or a transaction or series of related transactions in which more than fifty percent (50%) of the voting power of the Company is to be disposed of, other than as contemplated by this Agreement, or (iii) whereby the Company has agreed to or plans to any other form of liquidation, dissolution or winding up of the Company.

3.8 Obligations to Related Parties. There are no obligations of the Company to officers, directors, stockholders, or employees of the Company other than (a) for payment of salary for services rendered, (b) reimbursement for reasonable expenses incurred by officers of the Company on behalf of the Company, not in excess of $5,000 per person and (c) stock option agreements outstanding under any stock option plan approved by the Board of Directors of the Company. None of the officers, directors or stockholders of the Company or any members of their immediate families, are indebted to the Company. No officer, director or stockholder, or any member of their immediate families, is, directly or indirectly, interested in any material

contract with the Company (other than such contracts as relate to any such person’s ownership of capital stock or other securities of the Company).

3.9 Changes. Since the Statement Date there has not been:

(a) Any change in the assets, liabilities, financial condition or operations of the Company from that reflected in the Financial Statements, other than changes in the ordinary course of business, none of which individually or in the aggregate has had a material adverse effect on such assets, liabilities, financial condition or operations of the Company;

(b) Any resignation or termination of any officer, key employee or group of employees of the Company; and the Company, to the best of its knowledge, does not know of the impending resignation or termination of employment of any such officer, key employee or group of employees;

(c) Any material change, except in the ordinary course of business, in the contingent obligations of the Company by way of guaranty, endorsement, indemnity, warranty or otherwise;

(d) Any damage, destruction or loss, whether or not covered by insurance, materially and adversely affecting the assets, properties, business, operations or financial condition of the Company (as such business is presently conducted and as it is proposed to be conducted);

(e) Any waiver by the Company of a valuable right or of a debt owed to it;

(f) Any direct or indirect loans or guarantees made by the Company to any stockholder, employee, officer or director of the Company, other than advances made in the ordinary course of business;

(g) Any material change in any compensation arrangement or agreement with any employee, officer, director or stockholder;

(h) Any declaration or payment of any dividend or other distribution of the assets of the Company or any direct or indirect redemption, purchase or other acquisition of the Company’s capital stock by the Company;

(i) Any labor organization activity related to the Company;

(j) Any debt, obligation or liability incurred, assumed or guaranteed by the Company, except those for immaterial amounts and other liabilities incurred in the ordinary course of business;

(k) Any sale, assignment or transfer of any patents, trademarks, copyrights, trade secrets or other intangible assets;

(l) Any change in any material agreement, collaboration, partnership or arrangement to which the Company is a party or by which it is bound that materially and adversely affects the business, assets, liabilities, financial condition or operations of the Company (as such business is presently conducted and as it is proposed to be conducted);

(m) Any other event or condition of any character that, either individually or cumulatively, has materially and adversely affected the business, assets, liabilities, financial condition or operations of the Company (as such business is presently conducted and as it is proposed to be conducted);

(n) Any satisfaction or discharge of any lien, claim or encumbrance or payment of any obligation by the Company, except in the ordinary course of business and which is not material to the assets, properties, financial condition, operating results or business of the Company (as such business is presently conducted and as it is proposed to be conducted);

(o) Receipt of notice that there has been a loss of, or material order cancellation by, any major customer of the Company;

(p) Any mortgage, pledge, transfer of a security interest in, or lien, created by the Company, with respect to any of its material properties or assets, except liens for taxes not yet due or payable; or

(q) Any arrangement or commitment by the Company to do any of the acts described in subsection (a) through (p) above.

3.10 Title to Properties and Assets; Liens, Etc. The Company has good and marketable title to its properties and assets, including the properties and assets reflected in the most recent balance sheet included in the Financial Statements, and good title to its leasehold estates (except for leasehold improvements installed by the Company in connection with the lease dated October, 2003 with Metropolitan Life Insurance Company), in each case subject to no mortgage, pledge, lien, lease, encumbrance or charge, other than (a) those resulting from taxes that have not yet become delinquent, (b) minor liens and encumbrances that do not materially detract from the value of the property subject thereto or materially impair the operations of the Company, (c) liens arising from the Loan & Security Agreement dated February 12, 2004 with Lighthouse Capital Partners V, L.P. and the Master Security Agreement, dated as of October 25, 2005, with Oxford Finance Corporation, (d) liens arising from the Bridge Loan Agreement dated May 25, 2006, between the Company and the Investors (as defined therein), pursuant to the Security Agreement dated May 25, 2006 between the Company, the Investors (as defined therein) and the Collateral Agent (as defined therein) and (e) those that have otherwise arisen in the ordinary course of business which do not materially impair the Company’s ownership or use of such property or assets. The Company is in compliance with all material terms of each lease to which it is a party or is otherwise bound.

3.11 Intellectual Property. The Company owns or possesses sufficient legal rights to all patents, trademarks, service marks, trade names, copyrights, trade secrets, licenses, information and proprietary rights and processes necessary for the conduct of its business as currently conducted and as proposed to be conducted without any conflict with, or infringement

of, the rights of others. The Company owns or possesses sufficient legal rights to all patents, trademarks, service marks, formulae, trade names, copyrights, trade secrets, licenses, information and proprietary rights and processes necessary for the conduct of its business as currently conducted and as proposed to be conducted without any conflict with, or infringement of, the rights of others. There are no outstanding options, licenses, agreements, claims, encumbrances or shared ownership of interests of any kind relating to anything referred to above in this Section 3.11 that is to any extent owned by or exclusively licensed to the Company, nor is the Company bound by or a party to any options, licenses or agreements of any kind with respect to the patents, trademarks, service marks, trade names, domain names, copyrights, trade secrets, licenses, information, proprietary rights and/or processes of any other person or entity, except, in either case, for standard end-user, object code, internal-use software license and support/maintenance agreements. The Company has not received any communications alleging that the Company has violated or, by conducting its business as currently conducted and as proposed to be conducted, would violate any of the patents, trademarks, service marks, trade names, copyrights, trade secrets or other proprietary rights or processes of any other person or entity. The Company is not aware that any of the employees or independent contractors of the Company is obligated under any contract (including licenses, covenants or commitments of any nature) or other agreement, or subject to any judgment, decree or order of any court or administrative agency, that would interfere with the use of such employee’s or independent contractor’s best efforts to promote the interests of the Company or that would conflict with the Company’s business as currently conducted and as proposed to be conducted. To the knowledge of the Company, neither the execution or delivery of this Agreement, nor the carrying on of the Company’s business as currently conducted and as proposed to be conducted by the employees and independent contractors of the Company, nor the conduct of the Company’s business as currently conducted and as proposed to be conducted will conflict with or result in a breach of the terms, conditions or provisions of, or constitute a default under, any contract, covenant or instrument under which any such employee or independent contractor is now obligated. The Company does not believes it is or will be necessary to use any inventions of any of the employees of the Company (or persons the Company currently intends to hire) made prior to or outside the scope of their employment by the Company. Set forth in Section 3.11 of the Schedule of Exceptions is a listing of all patents and pending patent applications and registrations and applications for trademarks, copyrights and domain names of, or exclusively licensed to, the Company.

3.12 Compliance with Other Instruments. The Company is not in violation or default of any term of its Restated Charter or Bylaws, or of any material provision of any mortgage, indenture, contract, agreement, instrument or contract to which it is party or by which it is bound or of any judgment, decree, order or writ. The execution, delivery, and performance of and compliance with this Agreement, and the Related Agreements, and the issuance and sale of the Shares pursuant hereto and of the Conversion Shares pursuant to the Restated Charter, will not, with or without the passage of time or giving of notice, result in any such violation, or be in conflict with or constitute a default under any such term, or result in the creation of any mortgage, pledge, lien, encumbrance or charge upon any of the properties or assets of the Company or the suspension, revocation, impairment, forfeiture or nonrenewal of any permit, license, authorization or approval applicable to the Company, its business or operations or any of its assets or properties.

3.13 Litigation. There is no action, suit, proceeding or governmental investigation pending or, to the Company’s knowledge, currently threatened against the Company that questions the validity of this Agreement or the Related Agreements or the right of the Company to enter into any of such agreements, or to consummate the transactions contemplated hereby or thereby, or that would reasonably be expected to result, either individually or in the aggregate, in any material adverse change in the assets, condition or affairs or business as proposed to be conducted of the Company, financially or otherwise, or any change in the current equity ownership of the Company. The foregoing includes, without limitation, actions pending or, to the Company’s knowledge, threatened involving the prior employment of any of the Company’s employees, their use in connection with the Company’s business of any information or techniques allegedly proprietary to any of their former employers, or their obligations under any agreements with prior employers. The Company is not a party or subject to the provisions of any order, writ, injunction, judgment or decree of any court or government agency or instrumentality. There is no action, suit, proceeding or investigation by the Company currently pending or that the Company intends to initiate.

3.14 Taxes.

(a) Tax Definitions. For the purposes of this Agreement:

(i) “Tax” or “Taxes” shall mean any federal, state local or foreign income, gross receipts, license, payroll, employment, excise, severance, stamp, occupation, premium, windfall profits, environmental, customs duties, capital stock, franchise, profits, withholding, social security, unemployment, disability, real property, personal property, sales, use, transfer, registration, value added, alternative or add-on minimum, estimated, or other tax of any kind whatsoever, including any interest, penalty, or addition thereto, whether disputed or not.

(ii) “Tax Return” shall mean any return, declaration, report, claim for refund, or information return or statement relating to Taxes, including any schedule or attachment thereto, and including any amendment thereof.

(b) Tax Returns and Payments. The Company has filed all material Tax Returns required to be filed by it. These Tax Returns are true and correct in all material respects. All Taxes shown to be due and payable on such Tax Returns, on or before the Initial Closing, and, to the Company’s knowledge, all other Taxes due and payable by the Company, have been paid or will be paid prior to the time they become delinquent. The provision for Taxes as shown in the Financial Statements (as defined below) is adequate for Taxes due or accrued as of the date thereof. To the knowledge of the Company, there is no pending dispute with any taxing authority relating to any of such Tax Returns or any proposed liability for any material Taxes to be imposed upon the properties or assets of the Company. The Company has withheld or collected from each payment made to each of its employees the amount of all material Taxes, including, but not limited to, federal income taxes, Federal Insurance Contribution Act taxes and Federal Unemployment Tax Act taxes required to be withheld or collected therefrom, and has paid the same to the proper Tax receiving officers or authorized depositories. The Company has neither elected pursuant to the Internal Revenue Code of 1986, as amended (the “Code”) to be treated as an “S” corporation or a collapsible corporation pursuant to Section 341(f) or Section

1362(a) of the Code, nor has it made any other elections pursuant to the Code (other than elections which relate solely to matters of accounting, depreciation or amortization) which would have a material effect on the Company, its financial condition, its business as presently conducted or presently proposed to be conducted or any of its properties or material assets.

3.15 Employees. The Company has no collective bargaining agreements with any of its employees. There is no labor union organizing activity pending or, to the Company’s knowledge, threatened with respect to the Company. The Company is not a party to or bound by any currently effective employment contract, deferred compensation arrangement, bonus plan, incentive plan, profit sharing plan, retirement agreement, employment benefit plan described in section 3(2)(A) or Section 3(2)(B) of the Employment Retirement Income Security Act of 1974, or other employee compensation plan or agreement. To the Company’s knowledge, no employee, nor any consultant with whom the Company has contracted, is in violation of any term of any employment contract, proprietary information agreement or any other agreement relating to the right of any such individual to be employed by, or to contract with, the Company because of the nature of the business to be conducted by the Company; and to the Company’s knowledge, the performance of the Company’s contracts with its independent contractors, will not result in any such violation. The Company has not received any notice alleging that any such violation has occurred. The Company has complied in all material respects with all applicable state and federal equal employment opportunity and other laws related to employment and immigration insofar as non-compliance may create a Company liability. The Company is not a party to or bound by any currently effective employment contract, deferred compensation agreement, bonus plan, incentive plan, profit sharing plan, retirement agreement, or other employee compensation agreement.

3.16 Registration Rights and Voting Rights. Except as required pursuant to the Investor Rights Agreement, the Company is presently not under any obligation, and has not granted any rights, to register (as defined in Section 1.1 of the Investor Rights Agreement), including piggyback rights, any of the Company’s presently outstanding securities or any of its securities that may hereafter be issued. To the Company’s knowledge, except as contemplated in the Voting Agreement, no stockholder of the Company has entered into any agreement with respect to the voting of equity securities of the Company.

3.17 Compliance with Laws; Permits. The Company is not in violation of any applicable statute, rule, regulation, order or restriction of any domestic or foreign government or any instrumentality or agency thereof in respect of the conduct of its business or the ownership of its properties which violation would materially and adversely affect the business, assets, liabilities, financial condition or operations of the Company. No governmental orders, permissions, consents, approvals or authorizations are required to be obtained and no registrations or declarations are required to be filed in connection with the execution and delivery of this Agreement and the issuance of the Shares or the Conversion Shares, except such as has been duly and validly obtained or filed, or with respect to any filings that must be made after the Initial Closing, as will be filed in a timely manner. The Company has not been nor is in default in any respect under such franchises, permits, licenses or similar authority which default would materially and adversely affect the business, assets, liabilities, financial condition or operations of the Company.

3.18 Environmental and Safety Laws.

(a) The Company is, and at all times since inception has been, in compliance with all applicable environmental laws or regulations and orders of any governments or governmental authorities, and with all permits, certificates, approvals, licenses and other authorizations relating thereto, except for non-compliance that would not materially and adversely affect the business, assets, liabilities, financial condition or operations of the Company. The term “environmental laws or regulations” means those statutes and regulations governing: (i) air emissions, (ii) liquid discharges to streams, ponds, ditches or other surface waters, (iii) liquid discharges to ground waters, (iv) liquid discharges to publicly-owned treatment works, (v) disposal of solid and/or hazardous wastes, (vi) marking, maintenance and/or removal of electrical equipment containing PCBs, (vii) manufacture and/or construction (including renovation) involving asbestos materials, (viii) activities in or adjacent to fresh water wetlands, flood hazard areas, coastal zone management areas and/or historic preservation areas, (ix) registration, operation, testing and/or removal or replacement of storage tanks for petroleum products and/or hazardous substances, and (x) emergency, planning and community right-to-know laws, including submission of hazardous substance inventory information to any authorities under any applicable jurisdictions.

(b) Except in a manner that would not result in material liability to the Company, the Company has not caused, nor is it causing, any disposals, releases, or threatened releases of any Hazardous Materials (as defined below) on or under any properties that the Company (i) owns, leases, occupies or operates or (ii) previously owned, leased, occupied or operated.

(c) The Company has not either (i) arranged for the disposal or treatment of Hazardous Material at any facility or site owned or operated by another person from which facility or site there has been a release or there is a release or threatened release of a Hazardous Material, or (ii) accepted any Hazardous Material for transport to disposal or treatment facilities or other sites selected by the Company, from which facilities or sites there has been a release or there is a release or threatened release of a Hazardous Material.

(d) The Company has not installed, used, buried or removed any surface impoundment or underground tank or vessel or sump, drain or pipeline which holds or held Hazardous Materials on properties owned, leased, occupied or operated by the Company.

(e) There has been no claim, and there are no pending or threatened claims, including without limitation any litigation, administrative proceedings or investigations or any other actions, claims, demands, notices of potential responsibility or requests for information brought or threatened, against the Company alleging liability of the Company with respect to the presence, disposal, release or threatened release of any Hazardous Material on, from or under any of the properties referenced in (b) above or otherwise relating to potential environmental liabilities, or any settlement reached by the Company relating to any of the foregoing.

(f) From the date hereof through and including the Initial Closing, the Company shall immediately provide the Purchasers with a copy of any notice, citation or

complaint alleging that the Company is not in compliance with any environmental laws or regulations.

As used in this Agreement, “Hazardous Material” means any material, substance, waste or component thereof (whether a liquid, solid, or gas) that is prohibited, controlled, or regulated by any governmental entity having jurisdiction as a contaminant, pollutant, dangerous substance, toxic substance, hazardous waste, hazardous substance, hazardous material, dangerous good or petroleum, its derivatives, by-products or other hydrocarbons, pursuant to any applicable environmental or health and safety law, rule, or regulation.

3.19 Offering Valid. Assuming the accuracy of the representations and warranties of the Purchasers contained in Section 4.2, the offer, sale and issuance of the Shares and the Conversion Shares will be exempt from the registration requirements of the Securities Act, and will be exempt from registration, permit or qualification requirements of all applicable state securities laws. Neither the Company nor any agent on its behalf has solicited or will solicit any offers to sell or has offered to sell or will offer to sell all or any part of the Shares to any person or persons so as to bring the sale of such Shares by the Company within the registration provisions of the Securities Act or any state securities laws.

3.20 Full Disclosure. The Company has provided the Purchasers with all information requested by the Purchasers in connection with its decision to purchase the Shares, including all information the Company believes is reasonably necessary to make such investment decision. No certificates made or delivered in connection with this agreement or the Related Agreements contain any untrue statement of a material fact or omits to state a material fact necessary to make the statements herein or therein misleading.

3.21 Minute Books. The minute books of the Company made available to such Purchaser contain a complete summary of all meetings of directors and stockholders since the time of incorporation and reflect all transactions referred to in such minutes accurately in all material respects.

3.22 Real Property Holding Corporation. The Company is not a real property holding corporation within the meaning of Section 897(c)(2) of the Code and any regulations promulgated thereunder.

3.23 Executive Officers and Directors. To the knowledge of the Company no executive officer, person nominated to become an executive officer, director or person nominated to become a director of the Company (a) has filed a petition under the Federal bankruptcy laws or any state insolvency law, been adjudged a bankrupt or made a general assignment for benefit of creditors, or been an officer, director or principal of any entity that was reorganized in bankruptcy, adjudged a bankrupt or made a general assignment for benefit of creditors, (b) has been convicted in a criminal proceeding or is a named subject of a pending criminal proceeding (excluding minor traffic violations), (c) has been the subject of any professional disciplinary proceeding, (d) was the subject of any order, judgment, or decree, not subsequently reversed, suspended or vacated, of any court of competent jurisdiction or any Federal or State authority, permanently or temporarily enjoining such person from, or otherwise limiting, such person from any type of business practice, (e) has been suspended or expelled

from membership in any securities or commodities exchange, association of securities or commodities dealers or investment advisors, (f) has had a license or registration as a dealer, broker, investment advisor or salesman, futures commission merchant, associated person, commodity pool operator, or commodity trading advisor denied, suspended or revoked, (g) has been enjoined or restrained by any court or government agency from the issuance, sale or offer for sale of securities or commodities, rendering securities or commodities advice, handling or managing trading accounts, or continuing any practices in connection with securities or commodities, or (h) has used or been known by any other name.

3.24 Insurance. The Company has in full force and effect fire and casualty insurance policies, with extended coverage, sufficient in amount (subject to reasonable deductibles) to allow it to replace any of its properties that might be damaged or destroyed. The Company has in full force and effect products liability and errors and omissions insurance in amounts customary for companies similarly situated.

3.25 Regulatory Compliance. As to each of the products of the Company, including, without limitation, products or compounds currently under research and/or development by the Company or its Subsidiary, subject to the jurisdiction of the Food and Drug Administration (“FDA”) under the Federal Food, Drug and Cosmetic Act and the regulations thereunder (“FDCA”) (each such product, a “Life Science Product”), such Life Science Product is being researched, developed, manufactured, tested, distributed, studied and/or marketed in compliance in all material respects with all applicable requirements under the FDCA and similar laws and regulations applicable to such Life Science Product, including those relating to investigational use, premarket approval, good manufacturing practices, labeling, advertising, record keeping, filing of reports and security. The Company has not received any notice or other communication from the FDA or any other federal, state or foreign governmental entity (i) contesting the premarket approval of, the uses of or the labeling and promotion of any Life Science Product or (ii) otherwise alleging any violation by the Company of any law, regulation or other legal provision applicable to a Life Science Product. Neither the Company, nor to the Company’s knowledge, any officer, employee or agent of the Company has, with respect to a Life Science Product, (i) made an untrue statement of a material fact or fraudulent statement to the FDA or other federal, state or foreign governmental entity performing similar functions or (ii) failed to disclose a material fact required to be disclosed to the FDA or such other federal, state or foreign governmental entity.

4. Representations and Warranties of the Purchasers. Each Purchaser hereby represents and warrants to the Company as follows (such representations and warranties do not lessen or obviate the representations and warranties of the Company set forth in this Agreement):

4.1 Requisite Power and Authority. Such Purchaser has all necessary power and authority under all applicable provisions of law and regulations to execute and deliver this Agreement and the Related Agreements and to carry out their provisions. All action on such Purchaser’s part required for the lawful execution and delivery of this Agreement and the Related Agreements have been or will be effectively taken prior to the Closing. Upon their execution and delivery, this Agreement and the Related Agreements will be valid and binding obligations of the Purchaser, enforceable in accordance with their terms, except (a) as limited by applicable bankruptcy, insolvency, reorganization, moratorium or other laws of general

application affecting enforcement of creditors’ rights, (b) as limited by general principles of equity that restrict the availability of equitable remedies, and (c) to the extent that the enforceability of indemnification provisions may be limited by applicable laws.

4.2 Investment Representations. Such Purchaser understands that neither the Shares nor the Conversion Shares have been registered under the Securities Act. Such Purchaser also understands that the Shares are being offered and sold pursuant to an exemption from registration contained in the Securities Act based in part upon such Purchaser’s representations contained in the Agreement. Such Purchaser hereby represents and warrants as follows:

(a) Purchaser Bears Economic Risk. Such Purchaser has substantial experience in evaluating and investing in private placement transactions of securities in companies similar to the Company so that it is capable of evaluating the merits and risks of its investment in the Company and has the capacity to protect its own interests. Such Purchaser must bear the economic risk of this investment indefinitely unless the Shares (or the Conversion Shares) are registered pursuant to the Securities Act, or an exemption from registration is available. Such Purchaser understands that the Company has no present intention of registering the Shares, the Conversion Shares or any shares of its Common Stock. Such Purchaser also understands that there is no assurance that any exemption from registration under the Securities Act will be available and that, even if available, such exemption may not allow such Purchaser to transfer all or any portion of the Shares or the Conversion Shares under the circumstances, in the amounts or at the times such Purchaser might propose.

(b) Acquisition for Own Account. Such Purchaser is acquiring the Shares and the Conversion Shares for such Purchaser’s own account for investment only, and not with a view towards their distribution.

(c) Purchaser Can Protect Its Interest. Such Purchaser represents that by reason of its, or of its management’s, business or financial experience, such Purchaser has the capacity to protect its own interests in connection with the transactions contemplated in this Agreement, and the Related Agreements. Further, such Purchaser is aware of no publication of any advertisement in connection with the transactions contemplated in the Agreement.

(d) Accredited Investor. Such Purchaser represents that it is an accredited investor within the meaning of Regulation D under the Securities Act.

(e) Company Information. Such Purchaser has received and read the Financial Statements and has had an opportunity to discuss the Company’s business, management and financial affairs with directors, officers and management of the Company and has had the opportunity to review the Company’s operations and facilities. Such Purchaser has also had the opportunity to ask questions of and receive answers from, the Company and its management regarding the terms and conditions of this investment.

registration is available. Such Purchaser has been advised or is aware of the provisions of Rule 144, which permits limited resale of shares purchased in a private placement subject to the satisfaction of certain conditions, including, among other things: the availability of certain current public information about the Company, the resale occurring following the required holding period under Rule 144 and the number of shares being sold during any three-month period not exceeding specified limitations.

(g) Residence. The office or offices of such Purchaser in which its investment decision was made is located at the address of such Purchaser set forth on the signature page hereto.

4.3 Transfer Restrictions. Such Purchaser acknowledges and agrees that the Shares and, if issued, the Conversion Shares are subject to restrictions on transfer as set forth in the Investor Rights Agreement.

5. Conditions to Closing.

5.1 Conditions to the Purchasers’ Obligations at the Closing. The obligations of each Purchaser to purchase Shares at the Closing are subject to the satisfaction, at or prior to the Initial Closing Date, of the following conditions, the waiver of which shall not be effective against any Purchaser who does not consent in writing thereto:

(a) Representations and Warranties True; Performance of Obligations. The representations and warranties made by the Company in Section 3 shall be true and correct in all material respects as of the Initial Closing Date, with the same force and effect as if they had been made as of the Initial Closing Date, and the Company shall have performed all obligations and conditions herein required to be performed or observed by it on or prior to the Initial Closing.

(b) Consents, Permits, and Waivers. The Company shall have obtained any and all consents, permits and waivers necessary or appropriate for consummation of the transactions contemplated by the Agreement and the Related Agreements, except for such as may be properly obtained subsequent to the Initial Closing.

(c) Filing of Restated Charter. The Restated Charter shall have been filed with the Secretary of State of the State of Delaware and shall continue to be in full force and effect as of the Initial Closing Date.

(d) Compliance Certificate. The Company shall have delivered to each Purchaser a Compliance Certificate, executed by the President of the Company dated the Initial Closing Date, to the effect that the conditions specified in subsections (a), (b) and (c) of this Section 5.1 have been satisfied and that there has been no material adverse change in the business, operations, properties or assets of the Company since the Statement Date.

Company’s Bylaws as in effect at the time of the Initial Closing, (iii) resolutions approved by the Board of Directors authorizing the transactions contemplated hereby, (iv) resolutions approved by the Company’s stockholders authorizing the filing of the Restated Charter, and (v) good standing certificates (including tax good standing) with respect to the Company from the applicable authority(ies) in Delaware, California and any other jurisdiction in which the Company is qualified to do business, dated a recent date before the Initial Closing.

(f) Investor Rights Agreement. The Investor Rights Agreement substantially in the form attached hereto as Exhibit C shall have been executed and delivered by the parties thereto other than each Purchaser.

(g) Co-Sale Agreement. The Co-Sale Agreement substantially in the form attached hereto as Exhibit D shall have been executed and delivered by the parties thereto other than each Purchaser.

(h) Voting Agreement. The Voting Agreement substantially in the form attached hereto as Exhibit E shall have been executed and delivered by the parties thereto other than each Purchaser.

(i) Legal Opinion. Each Purchaser shall have received from legal counsel to the Company an opinion addressed to them, dated as of the Initial Closing Date, in substantially the form attached hereto as Exhibit F.

(j) Proceedings and Documents. All corporate and other proceedings in connection with the transactions contemplated at the Initial Closing hereby and all documents and instruments incident to such transactions shall be reasonably satisfactory in substance and form to each Purchaser and its special counsel, as applicable, and each Purchaser and its special counsel, as applicable, shall have received all such counterpart originals or copies of such documents as they may reasonably request.

(k) Performance of Obligations. The Company shall have performed and complied with all agreements and conditions herein required to be performed or complied with by the Company on or before the Initial Closing.

(l) Board of Directors. The Board shall consist of seven (7) members, which members shall be Xxxx Xxxx, Xxxxxxx Xxxxxx, Xxxxxx Xxxxxx, Xxxxxxx Xxxxxxx, Xxxxxxx Xxxxxx and Xxxxxx Xxxx. There shall be one vacancy on the Board.

(m) Amendment to Maxygen Agreement. The Company shall have entered into an amendment to the License Agreement, effective as of March 28, 2002, as amended, between Maxygen, Inc. and the Company.

5.2 Conditions to the Company’s Obligations at the Closing. The Company’s obligation to issue and sell the Shares at each Closing is subject to the satisfaction, on or prior to such Closing, of the following conditions:

(a) Representations and Warranties True. The representations and warranties in Section 4 made by each Purchaser shall be true and correct in all material respects as of the Closing, with the same force and effect as if they had been made on and as of that date.

(c) Performance of Obligations. The Purchasers shall have performed and complied with all agreements and conditions herein required to be performed or complied with by the Purchasers on or before the Closing.

(d) Filing of Restated Charter. The Restated Charter shall have been filed with the Secretary of State of the State of Delaware.

(e) Investor Rights Agreement. The Investor Rights Agreement substantially in the form attached hereto as Exhibit C shall have been executed and delivered by the parties thereto other than the Company.

(f) Co-Sale Agreement. The Co-Sale Agreement substantially in the form attached hereto as Exhibit D shall have been executed and delivered by the parties thereto other than the Company.

(g) Voting Agreement. The Voting Agreement substantially in the form attached hereto as Exhibit E shall have been executed and delivered by the parties thereto other than the Company.

6. Miscellaneous.

6.1 Governing Law. This Agreement shall be governed in all respects by the laws of the State of California as such laws are applied to agreements between California residents entered into and performed entirely in California.

6.2 Survival. The representations, warranties and agreements made herein shall survive the closing of the transactions contemplated hereby, and shall in no way be affected by any investigation of the subject matter thereof made by or on behalf of the Purchaser or the Company. All statements as to factual matters contained in any certificate or other instrument delivered by or on behalf of the Company pursuant hereto in connection with the transactions contemplated hereby shall be deemed to be representations and warranties by the Company hereunder solely as of the date of such certificate or instrument.

6.3 Successors and Assigns. Except as otherwise provided herein, the provisions hereof shall inure to the benefit of, and be binding upon, the successors, assigns, heirs, executors and administrators of the parties hereto; provided, however, that the rights of a Purchaser to purchase Shares shall not be assignable without the consent of the Company; provided, further, however, the rights under this Agreement may be assignable to any entity affiliated by common control (or other related entity) of a Purchaser. Nothing in this Agreement,

express or implied, is intended to confer upon any party other than the parties hereto or their respective successors and assigns and rights, remedies, obligations, or liabilities under or by reason of this Agreement, except as expressly provided by this Agreement.

6.4 Entire Agreement. This Agreement, the exhibits and schedules hereto, the Related Agreements and the other documents delivered pursuant hereto constitute the full and entire understanding and agreement between the parties with regard to the subjects hereof and no party shall be liable or bound to any other in any manner by any representations, warranties, covenants and agreements except as specifically set forth herein and therein.

6.5 Severability. In case any provision of the Agreement shall be invalid, illegal or unenforceable, the validity, legality and enforceability of the remaining provisions shall not in any way be affected or impaired thereby and this Agreement shall be construed as if such invalid, illegal or unenforceable provision had never been contained herein.

6.6 Amendment and Waiver. This Agreement may be amended or modified only upon the written consent of the Company and holders of at least sixty percent (60%) of the Common Stock issuable or issued upon the conversion of the Shares.

6.7 Delays or Omissions. It is agreed that no delay or omission to exercise any right, power or remedy accruing to any party, upon any breach, default or noncompliance by another party under this Agreement, the Related Agreements or the Restated Charter, shall impair any such right, power or remedy, nor shall it be construed to be a waiver of any such breach, default or noncompliance, or any acquiescence therein, or of or in any similar breach, default or noncompliance thereafter occurring. It is further agreed that any waiver, permit, consent or approval of any kind or character on the Purchaser’s part of any breach, default or noncompliance under this Agreement, the Related Agreements or under the Restated Charter or any waiver on such party’s part of any provisions or conditions of the Agreement, the Related Agreements, or the Restated Charter must be in writing and shall be effective only to the extent specifically set forth in such writing. All remedies, either under this Agreement, the Related Agreements, the Restated Charter, by law, or otherwise afforded to any party, shall be cumulative and not alternative.

6.8 Notices. All notices required or permitted hereunder shall be in writing and shall be deemed effectively given: (a) upon personal delivery to the party to be notified, (b) when sent by confirmed telex or facsimile if sent during normal business hours of the recipient, if not, then on the next business day, (c) five (5) days after having been sent by registered or certified mail, return receipt requested, postage prepaid, or (d) one (1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt. All communications shall be sent to the respective addresses of the parties as set forth on the signature page hereof or at such other address as the Company or the Purchasers may designate by ten (10) days advance written notice to the other party hereto.

6.9 Expenses. The Company and each Purchaser shall bear their own expenses and legal fees incurred on their behalf with respect to this Agreement and the transactions contemplated hereby; provided, however, that at the Initial Closing, the Company shall pay the reasonable and documented fees and expenses, not to exceed $120,000 in the

aggregate, of (i) Xxxxxxxxx Xxxxxxx Xxxxxx Xxxxxxxxxx Xxxxxxxx & Xxxxxxxxx, LLP, special counsel to Bio*One, and (ii) Xxxxx & Xxxxxxx XX, intellectual property counsel to Bio*One, in connection with the transactions contemplated by this Agreement.

6.10 Attorneys’ Fees. In the event that any suit or action is instituted to enforce any provision in this Agreement, the prevailing party in such dispute shall be entitled to recover from the losing party all fees, costs and expenses of enforcing any right of such prevailing party under or with respect to this Agreement, including without limitation, such reasonable fees and expenses of attorneys and accountants, which shall include, without limitation, all fees, costs and expenses of appeals.

6.11 Titles and Subtitles. The titles of the sections and subsections of the Agreement are for convenience of reference only and are not to be considered in construing this Agreement.

6.12 Counterparts. This Agreement may be executed in any number of counterparts and by facsimile, each of which shall be an original, but all of which together shall constitute one instrument.

6.13 Broker’s Fees. Each party hereto represents and warrants that no agent, broker, investment banker, person or firm acting on behalf of or under the authority of such party hereto is or will be entitled to any broker’s or finder’s fee or any other commission directly or indirectly in connection with the transactions contemplated herein. Each party hereto further agrees to indemnify each other party for any claims, losses or expenses incurred by such other party as a result of the representation in this Section 6.13 being untrue.

6.14 Pronouns. All pronouns contained herein, and any variations thereof, shall be deemed to refer to the masculine, feminine or neutral, singular or plural, as to the identity of the parties hereto may require.

6.15 California Corporate Securities Law. THE SALE OF THE SECURITIES WHICH ARE THE SUBJECT OF THIS AGREEMENT HAS NOT BEEN QUALIFIED WITH THE COMMISSIONER OF CORPORATIONS OF THE STATE OF CALIFORNIA AND THE ISSUANCE OF SUCH SECURITIES OR THE PAYMENT OR RECEIPT OF ANY PART OF THE CONSIDERATION THEREFOR PRIOR TO SUCH QUALIFICATION OR IN THE ABSENCE OF AN EXEMPTION FROM SUCH QUALIFICATION IS UNLAWFUL. PRIOR TO ACCEPTANCE OF SUCH CONSIDERATION BY THE COMPANY, THE RIGHTS OF ALL PARTIES TO THIS AGREEMENT ARE EXPRESSLY CONDITIONED UPON SUCH QUALIFICATION BEING OBTAINED OR AN EXEMPTION FROM SUCH QUALIFICATION BEING AVAILABLE.

(Signature Page Follows)

IN WITNESS WHEREOF, the parties hereto have executed this Series D Preferred Stock Purchase Agreement as of the date set forth in the first paragraph hereof.


CODEXIS, INC.

By:
Name:
Title:

SIGNATURE PAGE TO SERIES D PREFERRED STOCK PURCHASE AGREEMENT


PURCHASERS:

MAXYGEN, INC.

By:
Name:
Title:

CMEA VENTURES LIFE SCIENCES 2000, L.P.

By:
Name:
Title:

CMEA VENTURES LIFE SCIENCES 2000, CIVIL LAW PARTNERSHIP

By:
Name:
Title:

SIGNATURE PAGE TO SERIES D PREFERRED STOCK PURCHASE AGREEMENT


PEQUOT PRIVATE EQUITY FUND III, L.P.

By:		PEQUOT CAPITAL MANAGEMENT, INC., its investment manager


By:
Name:
Title:



PEQUOT OFFSHORE PRIVATE EQUITY PARTNERS III, L.P.



By:		PEQUOT CAPITAL MANAGEMENT, INC.,
		its investment manager


By:
Name:
Title:

CTTV INVESTMENTS LLC

By:
Name:
Title:

SIGNATURE PAGE TO SERIES D PREFERRED STOCK PURCHASE AGREEMENT

BIOMEDICAL SCIENCES INVESTMENT FUND PTE LTD



By:


Name:
Title:

XXXXXX X. XXXXXXX-XXXXX



By:


Name:

SIGNATURE PAGE TO SERIES D PREFERRED STOCK PURCHASE AGREEMENT


THE CONUS FUND, L.P.

By:
Name:
Title:

EAST XXXXXX INC. (BVI)

By:
Name:
Title:

THE CONUS FUND OFFSHORE LTD.

By:
Name:
Title:

THE CONUS FUND (QP) L.P.

By:
Name:
Title:

SIGNATURE PAGE TO SERIES D PREFERRED STOCK PURCHASE AGREEMENT

EQUILON ENTERPRISES LLC DBA SHELL OIL PRODUCTS US


By:
Name:
Title:

SIGNATURE PAGE TO SERIES D PREFERRED STOCK PURCHASE AGREEMENT

EXHIBIT A

SCHEDULE OF PURCHASERS

A-1

SCHEDULE B

Form of Series E Stock Purchase Agreement

CODEXIS, INC.

SERIES E PREFERRED STOCK PURCHASE AGREEMENT

November 13, 2007

TABLE OF CONTENTS


			Page
1.	Agreement to Sell and Purchase		1

	1.1	Authorization of Shares	1

	1.2	Sale and Purchase	1

2.	Closing, Delivery and Payment		1

	2.1	Closing	1

	2.2	Subsequent Closings	2

	2.3	Delivery	2

3.	Representations and Warranties of the Company		2

	3.1	Organization, Good Standing and Qualification	2

	3.2	Subsidiaries	3

	3.3	Capitalization; Voting Rights	3

	3.4	Authorization; Binding Obligations	5

	3.5	Financial Statements	5

	3.6	Liabilities	5

	3.7	Agreements; Action	5

	3.8	Obligations to Related Parties	6

	3.9	Changes	7

	3.10	Title to Properties and Assets; Liens, Etc.	8

	3.11	Intellectual Property	8

	3.12	Compliance with Other Instruments	9

	3.13	Litigation	10

	3.14	Taxes	10

	3.15	Employees	11

	3.16	Registration Rights and Voting Rights	11

	3.17	Compliance with Laws; Permits	11

	3.18	Environmental and Safety Laws	12

	3.19	Offering Valid	13

	3.20	Full Disclosure	13

	3.21	Minute Books	13

	3.22	Real Property Holding Corporation	13

	3.23	Executive Officers and Directors	13


	3.24	Insurance	14

	3.25	Regulatory Compliance	14

4.	Representations and Warranties of the Purchasers		14

	4.1	Requisite Power and Authority	15

	4.2	Investment Representations	15

	4.3	Transfer Restrictions	16

5.	Conditions to Closing		16

	5.1	Conditions to the Purchasers’ Obligations at the Closing	16

	5.2	Conditions to the Company’s Obligations at the Closing	17

6.	Miscellaneous		18

	6.1	Governing Law	18

	6.2	Survival	18

	6.3	Successors and Assigns	18

	6.4	Entire Agreement	19

	6.5	Severability	19

	6.6	Amendment and Waiver	19

	6.7	Delays or Omissions	19

	6.8	Notices	19

	6.9	Expenses	19

	6.10	Attorneys’ Fees	20

	6.11	Titles and Subtitles	20

	6.12	Counterparts	20

	6.13	Broker’s Fees	20

	6.14	Pronouns	20

	6.15	California Corporate Securities Law	20



EXHIBITS

Exhibit A				Schedule of Purchasers
Exhibit B				Sixth Amended and Restated Certificate of Incorporation
Exhibit C				Fourth Amended and Restated Investor Rights Agreement
Exhibit D				Third Amended and Restated Right of First Refusal and Co-Sale Agreement
Exhibit E				Fourth Amended and Restated Voting Agreement
Exhibit F				Form of Opinion of Xxxxxx & Xxxxxxx LLP

CODEXIS, INC.

SERIES E PREFERRED STOCK PURCHASE AGREEMENT

This Series E Preferred Stock Purchase Agreement (the “Agreement”) is made and entered into as of November 13, 2007, by and among Codexis, Inc., a Delaware corporation (the “Company”), and the purchasers, severally and not jointly, listed on Exhibit A hereto, each of which is herein referred to as a “Purchaser” and all of which are collectively referred to herein as the “Purchasers”.

Recitals

WHEREAS, the Company has authorized the sale and issuance of up to an aggregate of six million four hundred thirty-four thousand three hundred thirty-eight (6,434,338) shares of its Series E Preferred Stock (the “Shares”); and

WHEREAS, the Company desires to issue and sell the Shares to the Purchasers upon the terms and subject to the conditions set forth herein.

Agreement

1. Agreement to Sell and Purchase.

1.1 Authorization of Shares. On or prior to the Initial Closing (as defined in Section 2.1 below), the Company shall have authorized (a) the sale and issuance to the Purchasers of the Shares and (b) the issuance of such shares of Common Stock to be issued upon conversion of the Shares (the “Conversion Shares”). The Shares and the Conversion Shares shall have the rights, preferences, privileges and restrictions set forth in the Sixth Amended and Restated Certificate of Incorporation of the Company, in the form attached hereto as Exhibit B (the “Restated Charter”), which shall have been adopted by the Company and filed with the Secretary of State of the State of Delaware on or before the Initial Closing.

2. Closing, Delivery and Payment.

2.1 Closing. The initial closing of the sale and purchase of the Shares under this Agreement (the “Initial Closing”) shall take place at 11:00 a.m., Pacific Time, at the offices of Xxxxxx & Xxxxxxx LLP, 000 Xxxxx Xxxxx, Xxxxx Xxxx, XX 00000 on such date as the

Company and the Purchasers acquiring in the aggregate more than half of the Shares shall mutually agree, or at such other time, date and place as the Company and the Purchasers acquiring in the aggregate more than half of the Shares shall mutually agree (such date is hereinafter referred to as the “Initial Closing Date”).

2.2 Subsequent Closings. Subject to the terms and conditions of this Agreement, the Company may sell, on or before December 5, 2007, any unsold Shares (up to a maximum aggregate of six million four hundred thirty-four thousand three hundred thirty-eight (6,434,338) Shares at all Closings (as defined below), at the same price per share as the Shares sold at the Initial Closing to such other persons and entities as are determined by the Company and the Board of Directors of the Company (each such new investor, an “Additional Purchaser”), following the fulfillment or waiver of the conditions set forth in Section 5 hereof or at such other time and place as the Company and the Additional Purchaser(s) mutually agree upon, orally or in writing (each of which time and place is designated as a “Subsequent Closing,” and with the Initial Closing, each a “Closing”). Any Additional Purchaser shall be considered a “Purchaser” for purposes of this Agreement, and any Series E Preferred Stock so acquired by such Additional Purchaser shall be considered “Shares” for the purposes of this Agreement and all other agreements contemplated hereby upon execution by such Additional Purchaser of an appropriate counterpart signature page. Upon each such event, the Company shall prepare and distribute to the Purchasers (including the Additional Purchasers) a revised Exhibit A, which shall include the name of each Additional Purchaser and the number of shares of Series E Preferred Stock to be purchased by each Additional Purchaser. Upon the Subsequent Closing of the sale of shares of Series E Preferred Stock to any Additional Purchaser, such Additional Purchaser shall also, as evidenced by an applicable executed counterpart signature page, become a party to the Related Agreements (as defined below) and shall have the rights and obligations hereunder and thereunder. Each Subsequent Closing shall take place at the offices of Xxxxxx & Xxxxxxx LLP, 000 Xxxxx Xxxxx, Xxxxx Xxxx, Xxxxxxxxxx. The Purchasers hereby irrevocably waive any pre-emptive rights or rights of first offer, and related notice rights, they may possess now or hereafter with respect to sales of Series E Preferred Stock made pursuant to this Section 2.2.

2.3 Delivery. As soon as practicable following each Closing, upon the terms and subject to the conditions hereof, the Company will deliver to each Purchaser a certificate or certificates representing that number of Shares set forth opposite such Purchaser’s name on Exhibit A hereto against payment of the purchase price therefore by check, wire transfer, past services rendered, or any combination of the foregoing.

Agreement in the form attached hereto as Exhibit D (the “Co-Sale Agreement”) and the Fourth Amended and Restated Voting Agreement in the form attached hereto as Exhibit E (the “Voting Agreement”) (collectively, the “Related Agreements”), (iii) to issue and sell the Shares and the Conversion Shares, (iv) to carry out the provisions of this Agreement, the Related Agreements and the Restated Charter and (v) to carry on its business as presently conducted and as proposed to be conducted. The Company is duly qualified and is authorized to do business and is in good standing as a foreign corporation in all jurisdictions in which the nature of its activities and of its properties (both owned and leased) makes such qualification necessary, except for those jurisdictions in which failure to do so would not have a material adverse effect on the Company or its business.

3.3 Capitalization; Voting Rights.

(a) The authorized capital stock of the Company, immediately prior to the Initial Closing, consists of (i) sixty-two million (62,000,000) shares of Common Stock, par value $0.0001 per share, of which three million three hundred thirty-nine thousand seven hundred six (3,339,706) shares are issued and outstanding, and (ii) thirty-three million two hundred four thousand eight hundred eighty-six (33,204,886) shares of Preferred Stock, par value $0.0001 per share, six million (6,0000,000) of which are designated Series A Preferred Stock, all of which are issued and outstanding, eight million one hundred one thousand one hundred one (8,101,101) of which are designated Series B Preferred Stock, all of which are issued and outstanding, one million five hundred fourteen thousand six hundred forty-five (1,514,645) of which are designated Series C Preferred Stock, all of which are issued and outstanding, eleven million one hundred fifty-four thousand eight hundred two (11,154,802) of which are designated Series D Preferred Stock, ten million four hundred ninety-six thousand nine hundred seventy-three (10,496,973) of which are issued and outstanding, and six million four hundred thirty-four thousand three hundred thirty-eight (6,434,338) of which are designated Series E Preferred Stock, none of which are issued and outstanding. The Company has a right of first refusal over transfers of all outstanding shares of Common Stock.

(b) The Company has reserved 12,457,642 shares of Common Stock for issuance to officers, directors, employees and consultants of the Company pursuant to its 2002 Stock Plan duly adopted by the Board of Directors and approved by the Company’s stockholders, as amended (the “Stock Plan”) or other plans, agreements or arrangements approved by the Board of Directors. Of such reserved shares of Common Stock, 997,294 shares have been issued pursuant to exercised options, options to purchase 8,889,559 shares have been granted and are currently outstanding and 2,570,789 shares of Common Stock remain available for issuance pursuant to future grants under the Stock Plan. The Company has reserved (i) an aggregate of 46,176 shares of Common Stock for issuance to Lighthouse Capital Partners IV, L.P. and Lighthouse Capital Partners IV, L.P. pursuant to warrants dated February 12, 2004 (the “Lighthouse Warrants”), (ii) an aggregate maximum of 65,000 shares of Common Stock pursuant to the Non-Qualified Stock Option Agreement dated as of February 23, 2004 and Non-Qualified Stock Option Agreement dated as of January 1, 2005, each by and between the

Company and Xxxxxx & Xxxxxxx LLP (the “Xxxxxx Options”), (iii) 9,100 shares of Common Stock for issuance to Oxford Finance Corporation pursuant to a warrant dated October 25, 2005 (the “Oxford Warrant”), (iv) an aggregate of 323,569 shares of Series D Preferred Stock for issuance to certain investors of the Company pursuant to warrants dated May 25, 2006 (the “Bridge Warrants”), (v) 3,577 shares of Common Stock for issuance to Alexandria Equities, LLC pursuant to a warrant dated February 9, 2006 and (vi) an aggregate of 109,091 shares of Series D Preferred Stock for issuance to General Electric Capital Corporation and Oxford Finance Corporation pursuant to warrants dated September 28, 2007 (the “Loan Warrants”). At the Initial Closing, except for (i) outstanding options issued pursuant to the Stock Plan, the Lighthouse Warrants, the Xxxxxx Options, the Oxford Warrant, the Bridge Warrants, the Loan Warrants and as set forth on Section 3.3(b) of the Schedule of Exceptions or options that may be issued in the ordinary course of business after the date of this Agreement, (ii) the conversion privileges of the Preferred Stock and (iii) the rights granted pursuant to this Agreement and the Related Agreements, there are no outstanding options, warrants, rights (including conversion or preemptive rights and rights of first refusal), proxy or stockholder agreements, or agreements of any kind for the purchase or acquisition from the Company of any of its securities.

(f) No stock plan, stock purchase, stock option or other agreement or understanding between the Company and any holder of any securities or rights exercisable or

convertible for securities provides for acceleration or other changes in the vesting provisions or other terms of such agreement or understanding as the result of the occurrence of any event.

3.5 Financial Statements. The Company has provided to the Purchasers (a) its unaudited financial statements (balance sheet and income and cash flow statements) at December 31, 2005 and December 31, 2006 and (b) its unaudited financial statements balance sheet and income and cash flow statements) as, at and for the seven-month period ended July 31, 2007 (the “Statement Date”) (collectively, the “Financial Statements”). The Financial Statements, together with the notes thereto, are complete and correct in all material respects and have been prepared in accordance with generally accepted accounting principles in the United States (“GAAP”) consistently applied and present fairly the financial condition and position of the Company as of their respective dates; provided, however, that the unaudited Financial Statements are subject to normal recurring year-end audit adjustments (which will not be material either individually or in the aggregate), and do not contain all footnotes required under GAAP.

3.7 Agreements; Action.

(a) Except for the Related Agreements there are no agreements, understandings or proposed transactions between the Company and any of its officers, directors, affiliates or any affiliate thereof.

(b) There are no agreements, understandings, instruments, contracts or proposed transactions to which the Company is a party or by which it is bound, nor to its knowledge any judgments, orders, writs or decrees to which the Company is a party or by which it is bound, that may involve (i) obligations (contingent or otherwise) of, or payments to, the Company in excess of $250,000, or (ii) the transfer or license of any patent, copyright, trade secret or other proprietary right to or from the Company (other than licenses entered into in the ordinary course of business involving payments to the Company not exceeding $250,000), (iii) indemnification by the Company with respect to infringements of proprietary rights (other than indemnification obligations arising from purchase or license agreements entered into in the ordinary course of business), (iv) provisions restricting or affecting development, manufacture, or distribution of the Company’s products or services or proposed products or services or (v) any other material agreement.

(c) The Company has not (i) declared or paid any dividends, or authorized or made any distribution upon or with respect to any class or series of its capital stock, (ii) incurred or guaranteed any indebtedness for money borrowed or any other liabilities individually in excess of $250,000 or, in the case of indebtedness and/or liabilities individually less than $250,000, in excess of $500,000 in the aggregate, (iii) made any loans or advances to any person, other than ordinary advances for travel expenses, or (iv) sold, exchanged or otherwise disposed of any of its assets or rights, other than the sale of its inventory in the ordinary course of business.

(f) The Company has not engaged in the past three months in any discussion (i) with any representative of any corporation or corporations whereby the Company has agreed to or plans to consolidate or merge the Company with or into any such corporation or corporations, (ii) with any corporation, partnership, association or other business entity or any individual whereby the Company has agreed to or plans to sell, convey or dispose of all or substantially all of the assets of the Company or a transaction or series of related transactions in which more than fifty percent (50%) of the voting power of the Company is to be disposed of, other than as contemplated by this Agreement, or (iii) whereby the Company has agreed to or plans to engage in or pursue any other form of liquidation, dissolution or winding up of the Company.

stock option plan approved by the Board of Directors of the Company. None of the officers, directors or stockholders of the Company or any members of their immediate families, are indebted to the Company. No officer, director or stockholder, or any member of their immediate families, is, directly or indirectly, interested in any material contract with the Company (other than such contracts as relate to any such person’s ownership of capital stock or other securities of the Company).

3.9 Changes. Since the Statement Date there has not been:

(c) Any material change, except in the ordinary course of business, in the contingent obligations of the Company by way of guaranty, endorsement, indemnity, warranty or otherwise;

(e) Any waiver by the Company of a valuable right or of a debt owed to it;

(f) Any direct or indirect loans or guarantees made by the Company to any stockholder, employee, officer or director of the Company, other than advances made in the ordinary course of business;

(g) Any material change in any compensation arrangement or agreement with any employee, officer, director or stockholder;

(i) Any labor organization activity related to the Company;

(j) Any debt, obligation or liability incurred, assumed or guaranteed by the Company, except those for immaterial amounts and other liabilities incurred in the ordinary course of business;

(k) Any sale, assignment or transfer of any patents, trademarks, copyrights, trade secrets or other intangible assets;

(o) Receipt of notice that there has been a loss of, or material order cancellation by, any major customer of the Company;

(q) Any arrangement or commitment by the Company to do any of the acts described in subsection (a) through (p) above.

3.10 Title to Properties and Assets; Liens, Etc. The Company has good and marketable title to its properties and assets, including the properties and assets reflected in the most recent balance sheet included in the Financial Statements, and good title to its leasehold estates (except for leasehold improvements installed by the Company in connection with the lease dated October, 2003 with Metropolitan Life Insurance Company), in each case subject to no mortgage, pledge, lien, lease, encumbrance or charge, other than (a) those resulting from taxes that have not yet become delinquent, (b) minor liens and encumbrances that do not materially detract from the value of the property subject thereto or materially impair the operations of the Company, (c) liens arising from the Loan & Security Agreement dated February 12, 2004 with Lighthouse Capital Partners V, L.P. and the Master Security Agreement, dated as of October 25, 2005, with Oxford Finance Corporation, (d) liens resulting from the Loan and Security Agreement dated September 28, 2007, with General Electric Capital Corporation and Oxford Finance Corporation and (e) those that have otherwise arisen in the ordinary course of business which do not materially impair the Company’s ownership or use of such property or assets. The Company is in compliance with all material terms of each lease to which it is a party or is otherwise bound.

3.11 Intellectual Property. The Company owns or possesses sufficient legal rights to all patents, trademarks, service marks, trade names, copyrights, trade secrets, licenses,

information and proprietary rights and processes necessary for the conduct of its business as currently conducted and as proposed to be conducted without any conflict with, or infringement of, the rights of others. The Company owns or possesses sufficient legal rights to all patents, trademarks, service marks, formulae, trade names, copyrights, trade secrets, licenses, information and proprietary rights and processes necessary for the conduct of its business as currently conducted and as proposed to be conducted without any conflict with, or infringement of, the rights of others. There are no outstanding options, licenses, agreements, claims, encumbrances or shared ownership of interests of any kind relating to anything referred to above in this Section 3.11 that is to any extent owned by or exclusively licensed to the Company, nor is the Company bound by or a party to any options, licenses or agreements of any kind with respect to the patents, trademarks, service marks, trade names, domain names, copyrights, trade secrets, licenses, information, proprietary rights and/or processes of any other person or entity, except, in either case, for (a) standard end-user, object code, internal-use software license and support/maintenance agreements or (b) licenses or agreements entered into in the ordinary course of business involving payments to the Company not exceeding $250,000. The Company has not received any communications alleging that the Company has violated or, by conducting its business as currently conducted and as proposed to be conducted, would violate any of the patents, trademarks, service marks, trade names, copyrights, trade secrets or other proprietary rights or processes of any other person or entity. The Company is not aware that any of the employees or independent contractors of the Company is obligated under any contract (including licenses, covenants or commitments of any nature) or other agreement, or subject to any judgment, decree or order of any court or administrative agency, that would interfere with the use of such employee’s or independent contractor’s best efforts to promote the interests of the Company or that would conflict with the Company’s business as currently conducted and as proposed to be conducted. To the knowledge of the Company, neither the execution or delivery of this Agreement, nor the carrying on of the Company’s business as currently conducted and as proposed to be conducted by the employees and independent contractors of the Company, nor the conduct of the Company’s business as currently conducted and as proposed to be conducted will conflict with or result in a breach of the terms, conditions or provisions of, or constitute a default under, any contract, covenant or instrument under which any such employee or independent contractor is now obligated. The Company does not believe it is or will be necessary to use any inventions of any of the employees of the Company (or persons the Company currently intends to hire) made prior to or outside the scope of their employment by the Company. Set forth in Section 3.11 of the Schedule of Exceptions is a listing of all patents and pending patent applications and registrations and applications for trademarks, copyrights and domain names of, or exclusively licensed to, the Company.

Company or the suspension, revocation, impairment, forfeiture or nonrenewal of any permit, license, authorization or approval applicable to the Company, its business or operations or any of its assets or properties.

3.13 Litigation. There is no action, suit, proceeding or governmental investigation pending or, to the Company’s knowledge, currently threatened against the Company that questions the validity of this Agreement or the Related Agreements or the right of the Company to enter into any of such agreements, or to consummate the transactions contemplated hereby or thereby, or that would reasonably be expected to result, either individually or in the aggregate, in any material adverse change in the Company’s assets, condition or affairs or in its business as conducted or as proposed to be conducted, financially or otherwise, or any change in the current equity ownership of the Company. The foregoing includes, without limitation, actions pending or, to the Company’s knowledge, threatened involving the prior employment of any of the Company’s employees, their use in connection with the Company’s business of any information or techniques allegedly proprietary to any of their former employers, or their obligations under any agreements with prior employers. The Company is not a party or subject to the provisions of any order, writ, injunction, judgment or decree of any court or government agency or instrumentality. There is no action, suit, proceeding or investigation by the Company currently pending or that the Company intends to initiate.

3.14 Taxes.

(a) Tax Definitions. For the purposes of this Agreement:

including, but not limited to, federal income taxes, Federal Insurance Contribution Act taxes and Federal Unemployment Tax Act taxes required to be withheld or collected there from, and has paid the same to the proper Tax receiving officers or authorized depositories. The Company has neither elected pursuant to the Internal Revenue Code of 1986, as amended (the “Code”) to be treated as an “S” corporation or a collapsible corporation pursuant to Section 341(f) or Section 1362(a) of the Code, nor has it made any other elections pursuant to the Code (other than elections which relate solely to matters of accounting, depreciation or amortization) which would have a material effect on the Company, its financial condition, its business as presently conducted or presently proposed to be conducted or any of its properties or material assets.

3.15 Employees. The Company has no collective bargaining agreements with any of its employees. There is no labor union organizing activity pending or, to the Company’s knowledge, threatened with respect to the Company. The Company is not a party to or bound by any currently effective employment contract, deferred compensation arrangement, bonus plan, incentive plan, profit sharing plan, retirement agreement, employment benefit plan described in Section 3(2)(A) or Section 3(2)(B) of the Employment Retirement Income Security Act of 1974, or other employee compensation plan or agreement. To the Company’s knowledge, no employee, nor any consultant with whom the Company has contracted, is in violation of any term of any employment contract, proprietary information agreement or any other agreement relating to the right of any such individual to be employed by, or to contract with, the Company because of the nature of the business to be conducted by the Company; and to the Company’s knowledge, the performance of the Company’s contracts with its independent contractors, will not result in any such violation. The Company has not received any notice alleging that any such violation has occurred. The Company has complied in all material respects with all applicable state and federal equal employment opportunity and other laws related to employment and immigration insofar as non-compliance may create a Company liability. The Company is not a party to or bound by any currently effective employment contract, deferred compensation agreement, bonus plan, incentive plan, profit sharing plan, retirement agreement, or other employee compensation agreement.

Initial Closing, as will be filed in a timely manner. The Company has not been nor is in default in any respect under such franchises, permits, licenses or similar authority which default would materially and adversely affect the business, assets, liabilities, financial condition or operations of the Company.

3.18 Environmental and Safety Laws.

environmental liabilities, or any settlement reached by the Company relating to any of the foregoing.

(f) From the date hereof through and including the Initial Closing, the Company shall immediately provide the Purchasers with a copy of any notice, citation or complaint alleging that the Company is not in compliance with any environmental laws or regulations.

3.20 Full Disclosure. The Company has provided the Purchasers with all information requested by the Purchasers in connection with its decision to purchase the Shares, including all information the Company believes is reasonably necessary to make such investment decision. No representation or warranty of the Company contained in this Agreement, the schedules and exhibits attached hereto or any certificate furnished or to be furnished to the Purchasers at the Initial Closing, when read together, contains any untrue statement of a material fact or omits to state a material fact necessary to make the statements herein or therein misleading in light of the circumstances under which they were made.

3.22 Real Property Holding Corporation. The Company is not a real property holding corporation within the meaning of Section 897(c)(2) of the Code and any regulations promulgated thereunder.

reorganized in bankruptcy, adjudged a bankrupt or made a general assignment for benefit of creditors, (b) has been convicted in a criminal proceeding or is a named subject of a pending criminal proceeding (excluding minor traffic violations), (c) has been the subject of any professional disciplinary proceeding, (d) was the subject of any order, judgment, or decree, not subsequently reversed, suspended or vacated, of any court of competent jurisdiction or any Federal or State authority, permanently or temporarily enjoining such person from, or otherwise limiting, such person from any type of business practice, (e) has been suspended or expelled from membership in any securities or commodities exchange, association of securities or commodities dealers or investment advisors, (f) has had a license or registration as a dealer, broker, investment advisor or salesman, futures commission merchant, associated person, commodity pool operator, or commodity trading advisor denied, suspended or revoked, (g) has been enjoined or restrained by any court or government agency from the issuance, sale or offer for sale of securities or commodities, rendering securities or commodities advice, handling or managing trading accounts, or continuing any practices in connection with securities or commodities, or (h) has used or been known by any other name.

3.24 Insurance. The Company has in full force and effect fire and casualty insurance policies, with extended coverage, sufficient in amount (subject to reasonable deductibles) to allow it to replace any of its properties that might be damaged or destroyed. The Company has in full force and effect products liability and directors and officers insurance in amounts customary for companies similarly situated.

4.1 Requisite Power and Authority. Such Purchaser has all necessary power and authority under all applicable provisions of law and regulations to execute and deliver this Agreement and the Related Agreements and to carry out their provisions. All action on such Purchaser’s part required for the lawful execution and delivery of this Agreement and the Related Agreements have been or will be effectively taken prior to the Closing. Upon their execution and delivery, this Agreement and the Related Agreements will be valid and binding obligations of such Purchaser, enforceable in accordance with their terms, except (a) as limited by applicable bankruptcy, insolvency, reorganization, moratorium or other laws of general application affecting enforcement of creditors’ rights, (b) as limited by general principles of equity that restrict the availability of equitable remedies, and (c) to the extent that the enforceability of indemnification provisions may be limited by applicable laws.

(d) Accredited Investor. Such Purchaser represents that it is an accredited investor within the meaning of Regulation D under the Securities Act.

has had the opportunity to review the Company’s operations and facilities. Such Purchaser has also had the opportunity to ask questions of and receive answers from, the Company and its management regarding the terms and conditions of this investment.

(f) Rule 144. Such Purchaser acknowledges and agrees that the Shares, and, if issued, the Conversion Shares are “restricted securities” as defined in Rule 144 promulgated under the Securities Act as in effect from time to time and must be held indefinitely unless they are subsequently registered under the Securities Act or an exemption from such registration is available. Such Purchaser has been advised or is aware of the provisions of Rule 144, which permits limited resale of shares purchased in a private placement subject to the satisfaction of certain conditions, including, among other things: the availability of certain current public information about the Company, the resale occurring following the required holding period under Rule 144 and the number of shares being sold during any three-month period not exceeding specified limitations.

(g) Residence. The office or offices of such Purchaser in which its investment decision was made is located at the address of such Purchaser set forth on the signature page hereto.

5. Conditions to Closing.

(e) Secretary’s Certificate. Each Purchaser shall have received from the Company’s Secretary or Assistant Secretary, a certificate having attached thereto (i) the Company’s Certificate of Incorporation as in effect at the time of the Initial Closing, (ii) the Company’s Bylaws as in effect at the time of the Initial Closing, (iii) resolutions approved by the Board of Directors authorizing the transactions contemplated hereby, (iv) resolutions approved by the Company’s stockholders authorizing the filing of the Restated Charter, and (v) good standing certificates (including tax good standing) with respect to the Company from the applicable authority(ies) in Delaware, California and any other jurisdiction in which the Company is qualified to do business, dated a recent date before the Initial Closing.

(g) Co-Sale Agreement. The Co-Sale Agreement substantially in the form attached hereto as Exhibit D shall have been executed and delivered by the parties thereto other than each Purchaser.

(h) Voting Agreement. The Voting Agreement substantially in the form attached hereto as Exhibit E shall have been executed and delivered by the parties thereto other than each Purchaser.

(d) Filing of Restated Charter. The Restated Charter shall have been filed with the Secretary of State of the State of Delaware.

(f) Co-Sale Agreement. The Co-Sale Agreement substantially in the form attached hereto as Exhibit D shall have been executed and delivered by the parties thereto other than the Company.

(g) Voting Agreement. The Voting Agreement substantially in the form attached hereto as Exhibit E shall have been executed and delivered by the parties thereto other than the Company.

6. Miscellaneous.

aggregate, of one counsel to the Purchasers, in connection with the transactions contemplated by this Agreement.

6.11 Titles and Subtitles. The titles of the sections and subsections of the Agreement are for convenience of reference only and are not to be considered in construing this Agreement.

6.12 Counterparts. This Agreement may be executed in any number of counterparts and by facsimile, each of which shall be an original, but all of which together shall constitute one instrument.

(Signature Page Follows)

IN WITNESS WHEREOF, the parties hereto have executed this Series E Preferred Stock Purchase Agreement as of the date set forth in the first paragraph hereof.


CODEXIS, INC.

By:
Name:		Xxxx Xxxx
Title:		President


PURCHASERS:

CMEA VENTURES LIFE SCIENCES 2000, L.P.

By:
Name:
Title:

CMEA VENTURES LIFE SCIENCES 2000, CIVIL LAW PARTNERSHIP

By:
Name:
Title:


PURCHASERS:

CTTV INVESTMENTS LLC

By:
Name:
Title:


PURCHASERS:

XXXXXX X. XXXXXXX-XXXXX

By:
Name:


PURCHASERS:



EQUILON ENTERPRISES LLC DBA SHELL OIL PRODUCTS US



By:
Name:
Title:


PURCHASERS:

GPSF SECURITIES INC.

By:
Name:
Title:


PURCHASERS:

AFAC EQUITY, L.P.

By:
Name:		Xxxxx X. Xxxxx
Title:		Portfolio Manager

Address:

McKinsey & Company, Inc.

00 Xxxx 00xx Xxxxxx, 00xx Xxxxx

Xxx Xxxx, Xxx Xxxx, 00000

Office (000) 000-0000

Fax (000) 000-0000


PURCHASERS:

CONUS FUND QP L.P.

By:
Name:
Title:


PURCHASERS:



MALAYSIAN LIFE SCIENCES CAPITAL FUND, LTD.



By:		Malaysian Life Sciences Capital Fund Management Company Ltd, its Manager



By:
Name:		Xx. Xxxxx Xxxx Xxxx
Title:		Co-Chairman

SCHEDULE C

Form of Amended and Restated License Agreement

[SEE EXHIBIT 10.4A]

SCHEDULE D

Warrant Agreement

THIS SECURITY HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”). NO SALE OR DISPOSITION MAY BE EFFECTED WITHOUT THE PRIOR WRITTEN CONSENT OF THE COMPANY OR WITHOUT AN EFFECTIVE REGISTRATION STATEMENT RELATED THERETO OR AN OPINION OF COUNSEL FOR THE HOLDER, SATISFACTORY TO THE COMPANY, THAT SUCH REGISTRATION IS NOT REQUIRED UNDER THE ACT OR RECEIPT OF A NO-ACTION LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION.

THE SALE OF THESE SECURITIES HAS NOT BEEN QUALIFIED WITH ANY STATE SECURITIES AUTHORITIES. THE RIGHTS OF ALL PARTIES TO THIS WARRANT ARE EXPRESSLY CONDITIONED UPON SUCH QUALIFICATION BEING OBTAINED UNLESS THE SALE IS SO EXEMPT.

THIS WARRANT MAY NOT BE EXERCISED EXCEPT IN COMPLIANCE WITH ALL APPLICABLE FEDERAL AND STATE SECURITIES LAWS TO THE REASONABLE SATISFACTION OF THE COMPANY AND LEGAL COUNSEL FOR THE COMPANY.

Void after November 1, 2008

CODEXIS, INC.

WARRANT AGREEMENT

THIS CERTIFIES THAT, for value received, Equilon Enterprises LLC dba Shell Oil Products US, a Delaware limited liability company, having a place of business at 000 Xxxxxxxxx Xxxxxx, Xxxxxxx, Xxxxx 00000 (“Shell”) and its registered assigns (hereinafter called the “Holder”) is entitled to purchase from Codexis, Inc., a Delaware corporation (the “Company”) whose address is 000 Xxxxxxxxx Xxxxx, Xxxxxxx Xxxx, Xxxxxxxxxx 00000, at any time during the Term of the Warrant, as described in Section 2 hereof, a number of shares of the Company’s Series D Preferred Stock (the “Warrant Shares”) equal to the quotient obtained by dividing (A) $3,000,000 by (B) the Warrant Price (as defined below). This Warrant Agreement is a “Warrant Agreement” as defined in that certain Collaborative Research Agreement (the “Research Agreement”), dated as of November 1, 2006 by and among the Company and Shell. This Warrant may be exercised in whole or in part, at the option of the Holder of this Warrant, and the Holder is also entitled to exercise the other appurtenant rights, powers and privileges hereinafter set forth.

1. Warrant Price. The Warrant Price will be calculated as follows:

(a) In the event that the Company fails to achieve the Final Research Milestone (as defined in the Research Agreement) pursuant to the terms of the Research Agreement, the purchase price per share shall equal Three United States Dollars and Ninety-Seven Cents ($3.97); and

(b) In the event that the Company achieves the Final Research Milestone pursuant to the terms of the Research Agreement, the purchase price per share shall equal Seven United States Dollars ($7.00).

(c) In the event that the Company consummates a Change of Control Transaction (as defined below) with an entity other than Shell or a Shell Affiliate (as defined in the Research Agreement) prior to the Price Determination Date (as defined below), the purchase price per share shall equal Seven United States Dollars ($7.00).

Notwithstanding anything to the contrary, in the event that the Company and Shell enter into a subsequent research agreement for the use of the Codexis Technology (as defined in the Research Agreement) in the Energy Field (as defined in the Research Agreement), including without limitation an extension of the Research Agreement of greater than three (3) months duration, during the term of the Research Agreement (the “Deemed Milestone”), then the Final Research Milestone will be deemed to have been achieved for purposes of this Section 1.

2. Term. This Warrant shall be exercisable from the Price Determination Date (as defined below) through the earlier of (i) 5:00 p.m. Pacific Standard Time on November 1, 2008, (ii) the date of the closing of the Company’s initial public offering of its Common Stock, provided that the Warrant is exercised prior to such closing or (iii) the effective date (prior to the effective time) of (w) any consolidation or merger of the Company with or into another corporation (other than a merger with another corporation in which the Company is a continuing corporation and which does not result in any reclassification or change of outstanding securities issuable upon exercise of this Warrant), (x) any other corporate reorganization in which the Company shall not be the continuing or surviving entity of such consolidation, merger or reorganization, (y) any transaction in which in excess of 50% of the Company’s voting power is transferred or (z) any sale of all or substantially all of the stock or assets of the Company (such a transaction, a “Change of Control Transaction”) (such time period, the “Term of the Warrant”); provided that, if the Company consummates a Change of Control Transaction with an entity other than Shell or a Shell Affiliate prior to the Price Determination Date, this Warrant shall be exercisable on the effective date of such Change of Control Transaction at a purchase price per share equal to Seven United States Dollars ($7.00), as set forth in Section 1(c) above. For avoidance of doubt, if the Holder fails to exercise this Warrant during the Term of the Warrant, this Warrant, and all of the Holder’s rights hereunder, shall terminate after the Term of the Warrant. Notwithstanding anything to the contrary, in the event that the Company terminates the Research Agreement due to a material breach thereof by Shell, as of the effective date of such termination, this Warrant, and all of the Holder’s rights hereunder, shall terminate. For purposes of this Section 2, the “Price Determination Date” shall be the earlier of (A) the date on which the Company and Shell agree whether the Company has achieved the Final Research Milestone pursuant to the terms of the Research Agreement, and (B) the occurrence of the Deemed Milestone.

3. Method of Exercise; Payment; Issuance of New Warrant. Subject to Section 2 hereof, the purchase right represented by this Warrant may be exercised by the Holder, in whole or in part, by:

3.1 The surrender of this Warrant (with the Notice of Exercise form attached hereto as Attachment A and the Investment Representation Statement attached hereto as Attachment B duly executed) at the principal office of the Company; and

3.2 The payment to the Company, by check or wire transfer or any combination of the foregoing, of an amount equal to the then applicable Warrant Price per share multiplied by the number of Warrant Shares then being purchased.

If this Warrant should be exercised in part only, the Company shall, upon surrender of this Warrant, execute and deliver a new Warrant evidencing the rights of the Holder thereof to purchase the balance of the Warrant Shares purchasable hereunder. Upon receipt by the Company of this Warrant and such Notice of Exercise, together with, if applicable, the aggregate Warrant Price, at such office, or by the stock transfer agent or warrant agent of the Company at its office, the Holder shall be deemed to be the holder of record of the applicable Warrant Shares, notwithstanding that the stock transfer books of the Company shall then be closed or that certificates representing such Warrant Shares shall not then be actually delivered to the Holder. The Company shall pay any and all documentary stamp or similar issue or transfer taxes payable in respect of the issue or delivery of the Warrant Shares.

4. Stock Fully Paid; Reservation of Warrant Shares. All shares of stock which may be issued upon the exercise of the rights represented by this Warrant will, upon issuance, be fully paid and nonassessable, and free from all taxes, liens and charges with respect to the issue thereof. During the period within which the rights represented by this Warrant may be exercised, (i) the Company will at all times have authorized and reserved for the purpose of issue upon exercise of the purchase rights evidenced by this Warrant, a sufficient number of shares of its stock to provide for the exercise of the rights represented by this Warrant, and (ii) the issuance of such shares upon the exercise of the rights represented by this Warrant shall not be subject to preemptive rights of any stockholder of the Company or any other third party. In the event that there is an insufficient number of Warrant Shares reserved for issuance pursuant to the exercise of this Warrant, the Company will take appropriate action to authorize an increase in its capital stock to allow for such issuance or similar issuance acceptable to the Holder.

5. Adjustment of Warrant Price and Number of Warrant Shares. The number and kind of Warrant Shares purchasable upon the exercise of this Warrant and the Warrant Price shall be subject to adjustment from time to time upon the occurrence of certain events, as follows:

5.1 Subdivision or Combination of Warrant Shares. If the Company at any time while this Warrant remains outstanding and unexpired shall subdivide or combine its stock, the Warrant Price shall be proportionately decreased in the case of a subdivision or increased in the case of a combination.

5.2 Stock Dividends. If the Company at any time while this Warrant is outstanding and unexpired shall pay a dividend with respect to stock payable in, or make any other distribution with respect to stock (except any distribution specifically provided for in the foregoing Section 5.1) of, stock, then the Warrant Price shall be adjusted, from and after the date of determination of stockholders entitled to receive such dividend or distribution, to that price

determined by multiplying the Warrant Price in effect immediately prior to such date of determination by a fraction (i) the numerator of which shall be the total number of shares of stock outstanding immediately prior to such dividend or distribution, and (ii) the denominator of which shall be the total number of shares of stock outstanding immediately after such dividend or distribution.

5.3 Adjustment of Number of Warrant Shares. Upon each adjustment in the Warrant Price, the number of shares of stock purchasable hereunder shall be adjusted, to the nearest whole share, to the product obtained by multiplying the number of Warrant Shares purchasable immediately prior to such adjustment in the Warrant Price by a fraction, the numerator of which shall be the Warrant Price immediately prior to such adjustment and the denominator of which shall be the Warrant Price immediately thereafter.

6. Fractional Warrant Shares. No fractional Warrant Shares will be issued in connection with any exercise hereunder, but in lieu of such fractional shares the Company shall make a cash payment therefor upon the basis of the Warrant Price then in effect.

7. Compliance with Securities Act.

7.1 Compliance with Securities Act. The Holder, by acceptance hereof, agrees that this Warrant and the Warrant Shares are being acquired for investment and that he, she or it will not offer, sell or otherwise dispose of this Warrant or any Warrant Shares except under circumstances which will not result in a violation of the Securities Act of 1933, as amended (the “Act”). Upon exercise of this Warrant, the Holder hereof shall confirm in writing, in a form attached hereto as Attachment B, that the Warrant Shares so purchased are being acquired for investment and not with a view toward distribution or resale. In addition, the Holder shall provide such additional information regarding such Holder’s financial and investment background, as the Company may reasonably request, as is relevant for purposes of determining the Holder’s suitability with respect to a purchase of the Warrant Shares. This Warrant and all Warrant Shares (unless registered under the Act) shall be stamped or imprinted with a legend in substantially the following form:

THIS SECURITY HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”). NO SALE OR DISPOSITION MAY BE EFFECTED WITHOUT THE PRIOR WRITTEN CONSENT OF THE COMPANY AND WITHOUT AN EFFECTIVE REGISTRATION STATEMENT RELATED THERETO OR AN OPINION OF COUNSEL FOR THE HOLDER, SATISFACTORY TO THE COMPANY, THAT SUCH REGISTRATION IS NOT REQUIRED UNDER THE ACT OR RECEIPT OF A NO-ACTION LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION.

7.2 Conditions for Transfer. Neither this Warrant, the Warrant Shares nor the shares of Common Stock issuable upon conversion of the Warrant Shares may be transferred or assigned in whole or in part without compliance with all applicable federal and state securities laws by the transferor and the transferee (including the delivery of investment representation

letters and legal opinions satisfactory to the Company, if such are requested by the Company). Notwithstanding the foregoing, no investment representation letter or opinion of counsel shall be required for any transfer of this Warrant (or any portion thereof) or any shares of Series D Preferred Stock issued upon exercise hereof (or shares of Common Stock issuable upon conversion thereof) (i) in compliance with customary transactions pursuant to Rule 144 or Rule 144A of the Act, or (ii) by gift, will or intestate succession by the Holder to his or her spouse or lineal descendants or ancestors or any trust for any of the foregoing or by the Holder to its managers, partners, members, affiliates (as defined under Rule 404 promulgated under the Act) or subsidiaries, as applicable; provided, that in each of the foregoing cases, the transferee agrees in writing to be subject to the terms of this Section 7.2. In addition, if the holder of the Warrant (or any portion thereof) or any Series D Preferred Stock issued upon exercise hereof or any shares of Common Stock issuable upon conversion thereof delivers to the Company an unqualified opinion of counsel satisfactory to the Company that no subsequent transfer of such securities shall require registration under the Act, the Company shall, upon such contemplated transfer, promptly deliver new documents/certificates for such securities that do not bear the legend set forth in Section 7.1 above. Subject to the provisions of this Warrant with respect to compliance with the Act, title to this Warrant may be transferred by endorsement (by the Holder executing an assignment form) and delivery in the same manner as a negotiable instrument transferable by endorsement and delivery. Notwithstanding the foregoing, with respect to any offer, sale or other disposition of this Warrant or of securities into which this Warrant may be converted or for which it may be exercised, the Holder will give written notice to the Company, describing briefly the manner thereof. Unless the Company reasonably determines that such transfer would violate applicable securities laws, and notifies the Holder thereof within ten (10) business days after receiving notice of the transfer, the Holder may effect such transfer. Each Warrant thus transferred and each certificate representing the securities thus transferred shall bear a legend as to the applicable restrictions on transferability in order to ensure compliance with the Act, unless in the opinion of counsel for the Company, such legend is not required in order to ensure compliance with the Act. The Company may issue stop transfer instructions to its transfer agent in connection with such restrictions.

8. Rights of Stockholders. No Holder of this Warrant shall be entitled to vote or receive dividends or be deemed the holder of stock or any other securities of the Company which may at any time be issuable on the exercise hereof for any purpose, nor shall anything contained herein be construed to confer upon the Holder of this Warrant, as such, any of the rights of a stockholder of the Company or any right to vote for the election of directors or upon any matter submitted to stockholders at any meeting thereof, or to give or withhold consent to any corporate action (whether upon any recapitalization, issuance of stock, reclassification of stock, change of par value or change of stock to no par value, consolidation, merger, conveyance, or otherwise) or to receive notice of meetings, or to receive dividends or subscription rights or otherwise until this Warrant has been exercised and the Warrant Shares shall have become deliverable, as provided herein.

9. Stockholder Agreements. Upon exercise of this Warrant, the Holder agrees to execute and become a party to that certain Third Amended and Restated Voting Agreement, that certain Second Amended and Restated Right of First Refusal and Co-Sale Agreement, and that certain Third Amended and Restated Investor Rights Agreement, each made and entered into as of August 22, 2006 by and among the Company and certain stockholders of the Company.

10. Governing Law. The terms and conditions of this Warrant and all acts and transactions pursuant hereto and the rights and obligations of the parties hereto shall be governed, construed and interpreted in accordance with California law, without giving effect to principles of conflicts of law.

11. Miscellaneous. The headings in this Warrant are for purposes of convenience and reference only, and shall not be deemed to constitute a part hereof. Neither this Warrant nor any term hereof may be changed, waived, discharged or terminated orally, but only by an instrument in writing signed by the Company and the registered Holder. Upon any Acquisition (as defined in the Amended and Restated Certificate of Incorporation of the Company), or any stock dividend, combination, stock split, reclassification or recapitalization of the capital stock of the Company, or the Company’s initial public offering of its Common Stock, the Company shall provide to each Holder at such time, ten (10) days’ prior notice to the closing of such events. All notices and other communications from the Company to the Holder shall be delivered by hand or mailed by first class registered or certified mail, postage prepaid, to the address furnished to the Company in writing by the Holder.

(Remainder of Page Intentionally Left Blank)

IN WITNESS WHEREOF, the Company has caused this Warrant to be duly executed by its officers, thereunto duly authorized this first day of November, 2006.


CODEXIS, INC.

By:		/s/ Xxxx Xxxx
Name:		Xxxx Xxxx
Title:		President

SIGNATURE PAGE TO WARRANT

ATTACHMENT A

TO WARRANT AGREEMENT

NOTICE OF EXERCISE

TO:	CODEXIS, INC.

1. The undersigned hereby elects to purchase shares of Series D Preferred Stock of CODEXIS, INC. as defined in and pursuant to the terms of the attached Warrant, and tenders herewith payment of the purchase price of such shares in full, together with all applicable transfer taxes, if any.

2. Please issue a certificate or certificates representing said shares of stock in the name of the undersigned or in such other name as is specified below:


		Name:
		Address:

3. The undersigned represents that the aforesaid shares of stock are being acquired for the account of the undersigned for investment and not with a view to, or for resale in connection with, the distribution thereof and that the undersigned has no present intention of distributing or reselling such shares. In support thereof, the undersigned has executed an Investment Representation Statement attached hereto as Attachment B.


WARRANTHOLDER


(signature)


(title)

Date:

ATTACHMENT B

TO WARRANT AGREEMENT

INVESTMENT REPRESENTATION STATEMENT


PURCHASER	:

COMPANY	:	CODEXIS, INC.

SECURITY	:

AMOUNT	:

DATE	:

In connection with the purchase of the above-listed securities and underlying stock (the “Securities”), I, the Purchaser, represent to the Company the following:

(a) I am purchasing these Securities for my own account for investment purposes only and not with a view to, or for the resale in connection with, any “distribution” thereof for purposes of the Securities Act of 1933, as amended (“Act”).

(b) I understand that the Securities have not been registered under the Act in reliance upon a specific exemption therefrom, which exemption depends upon, among other things, the bona fide nature of my investment intent as expressed herein. In this connection, I understand that, in the view of the Securities and Exchange Commission (“SEC”), the statutory basis for such exemption may be unavailable if my representation was predicated solely upon a present intention to hold these Securities for the minimum capital gains period specified under tax statutes, for a deferred sale, for or until an increase or decrease in the market price of the Securities, or for a period of one year or any other fixed period in the future.

(c) I further understand that the Securities must be held indefinitely unless subsequently registered under the Act or unless an exemption from registration is otherwise available. Moreover, I understand that the Company is under no obligation to register the Securities. In addition, I understand that the certificate evidencing the Securities will be imprinted with a legend which prohibits the transfer of the Securities unless they are registered or such registration is not required in the opinion of counsel for the Company.

(d) I am aware of the provisions of Rule 144, promulgated under the Act, which, in substance, permits limited public resale of “restricted securities” acquired, directly or indirectly, from the issuer thereof (or from an affiliate of such issuer), in a non-public offering subject to the satisfaction of certain conditions.

(e) I further understand that at the time I wish to sell the Securities there may be no public market upon which to make such a sale.



WARRANTHOLDER


(signature)


(title)

Date:

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AMENDED AND RESTATED COLLABORATIVE RESEARCH AGREEMENT

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