CymaBay Therapeutics, Inc. Sample Contracts

CYMABAY THERAPEUTICS, INC., Issuer AND [TRUSTEE], Trustee INDENTURE Dated as of [●], 20 Debt Securities
Indenture • December 29th, 2017 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • New York

INDENTURE, dated as of [●], 20 , among CymaBay Therapeutics, Inc., a Delaware corporation (the “Company”), and [TRUSTEE], as trustee (the “Trustee”):

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CymaBay Therapeutics, Inc. Shares of Common Stock (par value $0.0001 per share) Controlled Equity OfferingSM Sales Agreement
Sales Agreement • July 2nd, 2020 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • New York

CymaBay Therapeutics, Inc., a Delaware corporation (the “Company”), confirms its agreement (this “Agreement”) with Cantor Fitzgerald & Co. (the “Agent”), as follows:

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•], AS WARRANT AGENT FORM OF PREFERRED STOCK WARRANT AGREEMENT DATED AS OF [•] CYMABAY THERAPEUTICS, INC. FORM OF PREFERRED STOCK WARRANT AGREEMENT
Preferred Stock Warrant Agreement • March 23rd, 2023 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • New York

THIS PREFERRED STOCK WARRANT AGREEMENT (this “Agreement”), dated as of [•], between CYMABAY THERAPEUTICS, INC. a Delaware corporation (the “Company”), and [•], a [corporation] [national banking association] organized and existing under the laws of [•] and having a corporate trust office in [•], as warrant agent (the “Warrant Agent”).

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•], AS WARRANT AGENT FORM OF COMMON STOCK WARRANT AGREEMENT DATED AS OF [•] CYMABAY THERAPEUTICS, INC. FORM OF COMMON STOCK WARRANT AGREEMENT
Common Stock Warrant Agreement • March 23rd, 2023 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • New York

THIS COMMON STOCK WARRANT AGREEMENT (this “Agreement”), dated as of [•], between CYMABAY THERAPEUTICS, INC. a Delaware corporation (the “Company”), and [•], a [corporation] [national banking association] organized and existing under the laws of [•] and having a corporate trust office in [•], as warrant agent (the “Warrant Agent”).

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CYMABAY THERAPEUTICS, INC. AND , AS WARRANT AGENT FORM OF DEBT SECURITIES WARRANT AGREEMENT DATED AS OF
Warrant Agreement • December 29th, 2017 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • New York

THIS DEBT SECURITIES WARRANT AGREEMENT (this “Agreement”), dated as of [●], between CYMABAY THERAPEUTICS, INC., a Delaware corporation (the “Company”) and [●], a [corporation] [national banking association] organized and existing under the laws of [●] and having a corporate trust office in [●], as warrant agent (the “Warrant Agent”).

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8,000,000 Shares CYMABAY THERAPEUTICS, INC. Common Stock UNDERWRITING AGREEMENT
Underwriting Agreement • March 6th, 2019 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • New York
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12,551,080 Shares1 Pre-Funded Warrants to Purchase Up to 583,771 Shares of Common Stock CymaBay Therapeutics, Inc. Common Stock PURCHASE AGREEMENT
Purchase Agreement • September 12th, 2023 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • New York

CymaBay Therapeutics, Inc., a Delaware corporation (the “Company”) proposes to sell to the several Underwriters named in Schedule I hereto (the “Underwriters”) an aggregate of 12,551,080 shares (the “Firm Shares”) of Common Stock, $0.0001 par value per share (the “Common Stock”), of the Company and pre-funded warrants (the “Warrants”) to purchase up to an aggregate of 583,771 shares of Common Stock in the form attached here to as Exhibit A. The Firm Shares consist of 12,551,080 authorized but unissued shares of Common Stock to be issued and sold by the Company. The Company has also granted to the several Underwriters an option to purchase up to 1,970,227 additional shares of Common Stock on the terms and for the purposes set forth in Section 3 hereof (the “Option Shares”). The Firm Shares and any Option Shares purchased pursuant to this Purchase Agreement (this “Agreement”) are herein collectively referred to as the “Shares.” The Shares and the Warrants are herein referred to as the “S

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LOAN AND SECURITY AGREEMENT
Loan and Security Agreement • October 17th, 2013 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations

THIS LOAN AND SECURITY AGREEMENT (as the same may from time to time be amended, modified, supplemented or restated, this “Agreement”) dated as of September 30, 2013 (the “Effective Date”) among SILICON VALLEY BANK, a California corporation with an office located at 3003 Tasman Drive, Santa Clara, CA 95054 (“Bank” or “SVB”), as collateral agent (in such capacity, “Collateral Agent”), the Lenders listed on Schedule 1.1 hereof or otherwise a party hereto from time to time including SVB in its capacity as a Lender and OXFORD FINANCE LLC, a Delaware limited liability company with an office located at 133 North Fairfax Street, Alexandria, Virginia 22314 (“Oxford”) (each a “Lender” and collectively, the “Lenders”), and CYMABAY THERAPEUTICS, INC., a Delaware corporation with offices located at 3876 Bay Center Place, Hayward, CA 94545 (“Borrower”), provides the terms on which the Lenders shall lend to Borrower and Borrower shall repay the Lenders. The parties agree as follows:

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INDEMNITY AGREEMENT
Indemnity Agreement • March 15th, 2018 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • Delaware

This Indemnity Agreement (this “Agreement”) dated as of ________ __, 20__, is made by and between CymaBay Therapeutics, Inc., a Delaware corporation (the “Company”), and _________________ (“Indemnitee”).

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LEASE by and between BMR-PACIFIC RESEARCH CENTER LP, a Delaware limited partnership and CYMABAY THERAPEUTICS, INC., a Delaware corporation
Lease • November 25th, 2013 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations

IN WITNESS WHEREOF, Tenant has executed this Acknowledgment of Term Commencement Date and Term Expiration Date as of the date first written above.

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CYMABAY THERAPEUTICS, INC. Shares of Common Stock (par value $0.0001 per share) Capital on Demand™ Sales Agreement
Capital on Demand Sales Agreement • May 11th, 2017 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • New York

CymaBay Therapeutics, Inc., a Delaware corporation (the “Company”), confirms its agreement (this “Agreement”) with JonesTrading Institutional Services LLC (the “Agent”), as follows:

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INDEMNITY AGREEMENT
Indemnification Agreement • September 19th, 2013 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • Delaware

THIS AGREEMENT is made and entered into this day of , 200 by and between METABOLEX, INC., a Delaware corporation (the “Corporation”), and (“Agent”).

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AGREEMENT AND PLAN OF MERGER among: CYMABAY THERAPEUTICS, INC., a Delaware corporation; GILEAD SCIENCES, INC., a Delaware corporation; and PACIFIC MERGER SUB, INC., a Delaware corporation Dated as of February 11, 2024
Merger Agreement • February 12th, 2024 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • Delaware

THIS AGREEMENT AND PLAN OF MERGER (“Agreement”) is made and entered into as of February 11, 2024 by and among: Gilead Sciences, Inc., a Delaware corporation (“Parent”); Pacific Merger Sub, Inc., a Delaware corporation and a wholly owned subsidiary of Parent (“Purchaser”); and CymaBay Therapeutics, Inc., a Delaware corporation (the “Company”). Certain capitalized terms used in this Agreement are defined in Exhibit A.

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CYMABAY THERAPEUTICS, INC. INDEMNITY AGREEMENT
Indemnification Agreement • October 17th, 2013 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • Delaware

THIS AGREEMENT is made and entered into this day of , 20 by and between CYMABAY THERAPEUTICS, INC., a Delaware corporation (the “Corporation”), and (“Agent”).

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11,600,000 Shares CYMABAY THERAPEUTICS, INC. Common Stock UNDERWRITING AGREEMENT
Underwriting Agreement • January 30th, 2018 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • New York
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5,181,348 Shares CYMABAY THERAPEUTICS, INC. Common Stock UNDERWRITING AGREEMENT
Underwriting Agreement • February 3rd, 2017 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • New York
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METABOLEX, INC. STOCK OPTION AGREEMENT (INCENTIVE STOCK OPTION OR NONSTATUTORY STOCK OPTION)
Stock Option Agreement • August 12th, 2013 • CymaBay Therapeutics, Inc.

Pursuant to your Stock Option Grant Notice (“Grant Notice”) and this Stock Option Agreement, Metabolex, Inc. (the “Company”) has granted you an option under its 2003 Equity Incentive Plan (the “Plan”) to purchase the number of shares of the Company’s Common Stock indicated in your Grant Notice at the exercise price indicated in your Grant Notice. Defined terms not explicitly defined in this Stock Option Agreement but defined in the Plan shall have the same definitions as in the Plan.

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LOAN AND SECURITY AGREEMENT
Loan and Security Agreement • November 12th, 2015 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations

THIS LOAN AND SECURITY AGREEMENT (as the same may from time to time be amended, modified, supplemented or restated, this “Agreement”) dated as of August 7, 2015 (the “Effective Date”) among OXFORD FINANCE LLC, a Delaware limited liability company with an office located at 133 North Fairfax Street, Alexandria, Virginia 22314 (“Oxford”), as collateral agent (in such capacity, “Collateral Agent”), the Lenders listed on Schedule 1.1 hereof or otherwise a party hereto from time to time including Oxford in its capacity as a Lender and SILICON VALLEY BANK, a California corporation with an office located at 3003 Tasman Drive, Santa Clara, CA 95054 (“Bank” or “SVB”) (each a “Lender” and collectively, the “Lenders”), and CYMABAY THERAPEUTICS, INC., a Delaware corporation with offices located at 7999 Gateway Blvd., Suite 130, Newark, CA 94560 (“Borrower”), provides the terms on which the Lenders shall lend to Borrower and Borrower shall repay the Lenders. The parties agree as follows:

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DEVELOPMENT AND CLINICAL MANUFACTURE AGREEMENT
Development and Clinical Manufacture Agreement • November 8th, 2013 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • New York

This Development and Clinical Manufacture Agreement (the “Agreement”) is made and entered into as of 30 April 2012 (the “Effective Date”) by and between METABOLEX, Inc., a Delaware corporation with its principal place of business located at 3876 Bay Center Place, Hayward, California 94545 (“METABOLEX”) and SIEGFRIED AG, a Swiss Company, with its principal address place of business located at Untere Brühlstrasse 4, Zofingen CH4800 Switzerland (“SIEGFRIED”). METABOLEX and SIEGFRIED may be referred to herein individually as a “Party” or collectively as the “Parties”.

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LICENSE AND DEVELOPMENT AGREEMENT
License and Development Agreement • November 8th, 2013 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • California

THIS LICENSE AND DEVELOPMENT AGREEMENT is made and entered into as of June 30, 1998 (the “Effective Date”) by and between METABOLEX, INC., a Delaware corporation with a place of business at 3876 Bay Center Place, Hayward, CA 94545 (“Metabolex”), and DIATEX, INC., a Texas corporation with a place of business at 105 Elm Spring Lane, San Antonio, TX 78231 (“DiaTex”). Metabolex and DiaTex may be referred to herein as a “Party” or, collectively, as “Parties.”

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DEVELOPMENT AND CLINICAL MANUFACTURE AGREEMENT
Development and Clinical Manufacture Agreement • November 8th, 2013 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • New York

This Development and Clinical Manufacture Agreement (the “Agreement”) is made and entered into as of June 5, 2012 (the “Effective Date”) by and between Metabolex, Inc., a Delaware corporation with its principal place of business located at 3876 Bay Center Place, Hayward, California 94545 (“Metabolex”) and Patheon Inc., a Canadian company with its principal place of business located at 2100 Syntex Court, Mississauga, Ontario, L5N 7K9, Canada (“Patheon”). Metabolex and Patheon may be referred to herein individually as a “Party” or collectively as the “Parties”.

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METRICS, INC. STANDARD DEVELOPMENT AGREEMENT
Standard Development Agreement • November 8th, 2013 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • Delaware

THIS AGREEMENT, effective as of October 31, 2006, by and between Metrics, Inc., a North Carolina corporation, having a principal place of business at 1240 Sugg Parkway, Greenville, NC 27834 (“METRICS”), and Metabolex, Inc., a Delaware corporation, having a principal place of business at 3876 Bay Center Place, Hayward, CA 94545 (“COMPANY”).

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FIRST AMENDMENT
License and Development Agreement • November 8th, 2013 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations

This First Amendment (the “First Amendment”), dated April 15, 1999, (“Effective Date of this First Amendment”) entered by and between Metabolex, Inc., a Delaware corporation with a place of business at 3876 Bay Center Place, Hayward, CA 94545 (“Metabolex”), and DiaTex, Inc., a Texas corporation with a place of business at 105 Elm Spring Lane, San Antonio, TX 78231 (“DiaTex”) amends the License and Development Agreement by and between the same Parties, dated June 30, 1998 (the “Agreement”). Metabolex and DiaTex may be referred to herein as a “Party” or, collectively, as “Parties.”

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PPAR-d LICENSE AGREEMENT
License Agreement • January 12th, 2018 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • California

THIS LICENSE AGREEMENT (the “Agreement”) is made and entered into as of the Effective Date (as defined below), by and between METABOLEX, INC., a Delaware corporation having its principal place of business at 3876 Bay Center Place, Hayward, CA 94545 (“Metabolex”), and JANSSEN PHARMACEUTICA NV, a corporation organized under the laws of Belgium having a place of business at 30 Turnhoutseweg, 2340 Beerse, Belgium (“Janssen”). Metabolex and Janssen are sometimes referred to herein individually as a “Party” and collectively as the “Parties.”

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Contract
Lease Agreement • August 12th, 2013 • CymaBay Therapeutics, Inc.

AMENDMENT NUMBER THREE to be attached to and form a part of the Lease (which together with any amendments, modifications and extensions hereto are hereinafter called the Lease), made the 18th day of February, 1992:

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Exclusive License Agreement between CymaBay Therapeutics, Inc. (as the licensor) and Kowa Pharmaceuticals America, Inc. (as the licensee) dated as of December 30, 2016
Exclusive License Agreement • March 23rd, 2017 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • New York

This Exclusive License Agreement (this “Agreement”) dated as of this 30th day of December, 2016 (the “Effective Date”), is between CymaBay Therapeutics, Inc., a Delaware corporation having offices located at 7999 Gateway Blvd., Suite 130, Newark, California, U.S.A. (“CymaBay”), and Kowa Pharmaceuticals America, Inc., a Delaware corporation having offices located at 530 Industrial Park Blvd., Montgomery, Alabama, U.S.A. (“Kowa”). Each of CymaBay and Kowa may be referred to hereinafter individually as a “Party” and together as the “Parties.”

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Re: Resignation Agreement
Resignation Agreement • October 17th, 2013 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • California

This letter sets forth the substance of the Resignation Agreement (the “Agreement”) that Metabolex, Inc. (the “Company”) is offering you as an alternative to the proposed Termination Agreement of today’s date.

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FIRST AMENDMENT TO LEASE
Lease • May 8th, 2018 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations
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SIXTH AMENDMENT TO LEASE
Lease • August 12th, 2013 • CymaBay Therapeutics, Inc.

THIS AMENDMENT, dated this 29th day of September, 2006, between RREEF AMERICA REIT II CORP. LLL, a Maryland corporation (“Landlord”) and METABOLEX, INC, a Delaware corporation (“Tenant”), for the premises located in the City of Hayward, County of Alameda, State of California, commonly known as 3876 Bay Center Place (the “Premises”), located in the building commonly known as Building D (“the Building”) in the project commonly known as Bay Center Business Park II, Hayward, California, (“the Project”).

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Re: Notice of Resignation and Transition Agreement
Transition Agreement • February 23rd, 2023 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations

This letter agreement sets forth your formal notice of resignation and the substance of a transition agreement (the “Agreement”) between CymaBay Therapeutics, Inc. (“CymaBay”) and you, entered into as a result of your resignation. The parties acknowledge that you are leaving your employment with CymaBay pursuant to Section 8.1 of your Employment Offer Letter dated May 5, 2021 (the “Employment Letter”) based on your own choice to pursue other endeavors. As a result, you are not entitled to any of the severance benefits set forth in Section 8.3 of the Employment Letter. However, in consideration of CymaBay continuing to provide employment benefits (including salary) to you from this date until May 17, 2023 (the “Transition Period”) and the other benefits set forth in this Agreement, you agree to provide the release set forth in Paragraph 12 hereof, as well as provide the other benefits to CymaBay set forth in this Agreement.

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REGISTRATION RIGHTS AGREEMENT
Registration Rights Agreement • October 17th, 2013 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • New York

This Agreement is made in connection with the offering contemplated by (i) the Securities Purchase Agreement dated as of the date hereof among the Company and certain purchasers (the “Purchase Agreement”), (ii) the several Subscription Agreements between the Company, on the one hand, and certain subscribers, on the other hand (the “Subscription Agreement”), and, (iii) if applicable, the Institutional Purchase Agreement (as defined in the Subscription Agreement) by and among the Company and certain purchasers (the Purchase Agreement, Subscription Agreement and Institutional Purchase Agreement shall collectively be referred to herein as the “Applicable Agreements”).

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SECOND AMENDMENT
Second Amendment • March 23rd, 2017 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations

THIS SECOND AMENDMENT (the “2nd Amendment”) is made and entered into effective as of December 23, 2016 (the “2nd Amendment Effective Date”) by and between CYMABAY THERAPEUTICS, INC., a Delaware corporation having a place of business at 7999 Gateway Blvd., Suite 130, Newark, CA 94560 USA (“CymaBay”), and DIATEX, INC., a corporation organized under the laws of Texas with a place of business at 105 Elm Spring Lane, San Antonio, TX 78231 (“DiaTex”). CymaBay and DiaTex may be referred to herein individually as a “Party”, and collectively as the “Parties.”

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SECOND AMENDMENT TO LEASE
Lease • February 28th, 2024 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations

THIS SECOND AMENDMENT TO LEASE (this “Amendment”) is entered into as of this 6th day of February, 2024, by and between BMR-PACIFIC RESEARCH CENTER LP, a Delaware limited partnership (“Landlord”), and CYMABAY THERAPEUTICS, INC., a Delaware corporation (“Tenant”).

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Contract
Lease • August 12th, 2013 • CymaBay Therapeutics, Inc.

AMENDMENT NUMBER TWO to be attached to and form a part of the Lease (which together with any amendments, modifications and extensions hereto are hereinafter called the Lease), made the 18th day of February, 1992:

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MASTER SERVICES AGREEMENT
Master Services Agreement • April 8th, 2014 • CymaBay Therapeutics, Inc. • Pharmaceutical preparations • New York

This Master Services Agreement (the “Agreement”) is entered into as of the last date of authorized signature contained herein (the “Effective Date”) by and between CYMABAY THERAPEUTICS, INC., with its principal place of business at 7999 Gateway Blvd., Ste. 130, Newark, CA 94560 (“CymaBay”) and INC RESEARCH, LLC, with its principal place of business at 3201 Beechleaf Court, Suite 600, Raleigh, NC 27604 (“INC RESEARCH”). INC Research, together with its Affiliates, are referred to herein as “CRO”. “Affiliate” means a person, corporation, partnership, or other entity that controls, is controlled by, or is under common control with a party, with the word “control” for purposes of this definition (including, with correlative meaning, the terms “controlled by” or “under common control with”) meaning the actual power, either directly or indirectly through one or more intermediaries, to direct the management and policies of such entity, whether by the ownership of at least fifty percent (50%) o

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