SGX Pharmaceuticals, Inc. Sample Contracts

UNDERWRITING AGREEMENT
Underwriting Agreement • January 4th, 2006 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations • New York
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LEASE
Lease • September 2nd, 2005 • SGX Pharmaceuticals, Inc. • California
UNDERWRITING AGREEMENT
Underwriting Agreement • September 2nd, 2005 • SGX Pharmaceuticals, Inc. • New York
1. PURPOSE
Memorandum of Understanding • September 2nd, 2005 • SGX Pharmaceuticals, Inc.
STRUCTURAL GENOMIX, INC.
Investor Rights Agreement • September 2nd, 2005 • SGX Pharmaceuticals, Inc. • California
BACKGROUND
Collaboration Agreement • November 14th, 2005 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations • Delaware
EXHIBIT 10.36 AMENDMENT TO AGREEMENT
Amendment to Agreement • November 14th, 2005 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations
Exhibit 10.31 MASTER LOAN AND SECURITY AGREEMENT NO. 2081008 DATED: AUGUST 28, 2002
Master Loan and Security Agreement • September 2nd, 2005 • SGX Pharmaceuticals, Inc.
BACKGROUND
Collaboration and License Agreement • November 14th, 2005 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations • Delaware
RECITALS
Indemnification Agreement • September 2nd, 2005 • SGX Pharmaceuticals, Inc. • Delaware
BACKGROUND
Collaboration Agreement • September 2nd, 2005 • SGX Pharmaceuticals, Inc. • Delaware
CHANGE IN CONTROL SEVERANCE AGREEMENT
Change in Control Severance Agreement • March 30th, 2007 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations • California

This Change in Control Severance Agreement (this “Agreement”) is entered into as of December 18, 2006 (the “Effective Date”), by and between Annette North (the “Executive”) and SGX Pharmaceuticals, Inc., a Delaware corporation (the “Company”).

Agreement and Plan of Merger dated as of July 8, 2008 among Eli Lilly and Company, REM Merger Sub, Inc. and SGX Pharmaceuticals, Inc.
Merger Agreement • July 8th, 2008 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations • Delaware

Agreement and Plan of Merger (this “Agreement”), dated as of July 8, 2008, among Eli Lilly and Company, an Indiana corporation (“Parent”), REM Merger Sub, Inc., a Delaware corporation and wholly-owned subsidiary of Parent (“Merger Sub”), and SGX Pharmaceuticals, Inc., a Delaware corporation (the “Company”).

23 JULY 2004
Patent and Know How License • January 4th, 2006 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations • Georgia
RECITALS
Drug Discovery Agreement • January 4th, 2006 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations • Maryland
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OSI Pharmaceuticals, Inc. 58 South Service Road, Suite 110 Melville, NY 11747 T 631.962.2000 F 631.752.3880 www.osip.com [(OSI)(TM) PHARMACEUTICALS LOGO)] January 11, 2004 VIA FEDERAL EXPRESS Sean A. McCarthy, D.Phil. Vice President, Business...
Collaboration Agreement • September 2nd, 2005 • SGX Pharmaceuticals, Inc.

This letter confirms acceptance by Structural GenomiX of an amendment to Section 2.8(b) of the above-referenced Collaboration Agreement whereby effective immediately, OSI Pharmaceuticals shall have the option to increase its membership on the Joint Steering Committee (JSC) to three (3) representatives, one of whom shall be a non-voting representative.

March 27, 2006 LICENSE AND COLLABORATION AGREEMENT Between NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH, INC. and SGX PHARMACEUTICALS, INC.
License and Collaboration Agreement • April 5th, 2006 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations • New York

This License and Collaboration Agreement (“Agreement”) is made as of this 27 day of March, 2006 (the “Effective Date”) by and between Novartis Institutes for BioMedical Research, Inc., a corporation organized and existing under the laws of the State of Delaware (“Novartis”) and SGX Pharmaceuticals, Inc., a corporation organized and existing under the laws of the State of Delaware (“SGX”). Novartis and SGX are each referred to individually as a “Party” and together as the “Parties.” Capitalized terms used but not otherwise defined herein have the meanings given to them in Section 1 hereof.

TERMINATION AGREEMENT
Termination Agreement • March 13th, 2006 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations

This Termination Agreement (the “Termination Agreement”) is made and entered into effective as of February 15, 2006 (the “Termination Effective Date”), by and between SGX Pharmaceuticals, Inc., (formerly known as Structural GenomiX, Inc.) a corporation incorporated under the laws of the State of Delaware and with its principal place of business located at 10505 Roselle Street, San Diego, CA 92121 (“SGX”) and Pierre Fabre Medicament S.A., (successor in interest to UroGene SA) a corporation incorporated under the laws of France with its registered office at 45, place Abel-Gance, 92654 Boulogne Cedex France (“PFM”). PFM and SGX may be referred to herein as a “Party” or, collectively, as “Parties”.

FIRST AMENDMENT TO THE DRUG DISCOVERY AGREEMENT
Drug Discovery Agreement • March 30th, 2007 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations

This First Amendment is entered into by and between SGX Pharmaceuticals, Inc., (formerly known as Structural GenomiX, Inc.) (“SGX”) and Cystic Fibrosis Foundation Therapeutics, Inc. (“CFFT”) and is effective as of March 1, 2007 (“Amendment Effective Date”). Collectively, SGX and CFFT are referred to hereinafter as the “Parties”.

FOURTH AMENDMENT TO LEASE AGREEMENT
Lease Agreement • March 30th, 2007 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations

THIS FOURTH AMENDMENT TO LEASE AGREEMENT (this “Fourth Amendment”) is made as of March 28, 2007, by and between ARE-10505 ROSELLE STREET, LLC, a Delaware limited liability company (“Landlord”), and SGX PHARMACEUTICALS, INC., a Delaware corporation, formerly known as Structural Genomix, Inc. (“Tenant”).

AMENDMENT TO AGREEMENT
Amendment to Agreement • December 12th, 2007 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations

This Amendment to Agreement (the “Amendment”) is made and entered into effective as of December 7, 2007 (the “Amendment Effective Date”), by and between SGX Pharmaceuticals, Inc. (formerly known as Structural GenomiX, Inc.), a corporation organized and existing under the laws of the State of Delaware and having its principal place of business located at 10505 Roselle Street, San Diego, CA 92121 (“SGX”) and Eli Lilly and Company., a corporation organized and existing under the laws of the state of Indiana and having its principal place of business at Lilly Corporate Center, Indianapolis, Indiana 46285, (“Lilly”). Lilly and SGX may be referred to herein as a “Party” or, collectively, as “Parties”.

EXHIBIT 99.1 The shares reported in this Form 3 are held directly by various subsidiaries of Credit Suisse, a Swiss bank. Mr. Vijay Lathi is a Managing Director of New Leaf Venture Partners, L.L.C. (NLV). NLV has entered into an agreement (the...
Sub-Management Agreement • January 31st, 2006 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations

The shares reported in this Form 3 are held directly by various subsidiaries of Credit Suisse, a Swiss bank. Mr. Vijay Lathi is a Managing Director of New Leaf Venture Partners, L.L.C. (NLV). NLV has entered into an agreement (the Agreement) with DLJ Capital Corporation (DLJCC), a Delaware corporation and indirect subsidiary of Credit Suisse that directly owns some of the shares as to which this Form 3 relates. Pursuant to the Agreement, NLV provides sub-management services for the Sprout investment portfolio. Mr. Lathi may be deemed to beneficially own the shares as to which this Form 3 relates. Mr. Lathi disclaims beneficial ownership of the shares except to the extent of his

Contract
Warrant Agreement • May 15th, 2007 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations • California

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AND PURSUANT TO THE PROVISIONS OF ARTICLE 5 BELOW, MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND APPLICABLE STATE SECURITIES LAW OR, IN THE OPINION OF LEGAL COUNSEL IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER OF THESE SECURITIES, SUCH OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION IS EXEMPT FROM REGISTRATION.

THIRD AMENDMENT TO LEASE (10575/10581 ROSELLE STREET)
Lease • December 21st, 2007 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations

THIS THIRD AMENDMENT TO LEASE (“Third Amendment”) is made and entered into as of the 21st day of December, 2007, by and between BRS TORREY I, LLC, a Delaware limited liability company (“Landlord”) and SGX PHARMACEUTICALS, INC., a Delaware corporation (“Tenant”).

THIRD AMENDMENT TO LEASE AGREEMENT
Lease Agreement • December 13th, 2007 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations

THIS THIRD AMENDMENT TO LEASE AGREEMENT (this “Third Amendment”) is made as of December 10, 2007, by and between ARE-3770 TANSY STREET, LLC, a Delaware limited liability company (“Landlord”), and SGX PHARMACEUTICALS, INC., a Delaware corporation (“Tenant”), formerly known as STRUCTURAL GENOMIX, INC.

BACKGROUND
Collaboration Agreement • November 14th, 2005 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations • Delaware
First Amendment to Amended and Restated Investor Rights Agreement
Investor Rights Agreement • March 31st, 2006 • SGX Pharmaceuticals, Inc. • Pharmaceutical preparations • California

This First Amendment to the Amended and Restated Investor Rights Agreement (the “Amendment”) is made effective as of October 31, 2005, and is entered into by and among SGX Pharmaceuticals, Inc., a Delaware corporation, previously known as Structural GenomiX, Inc. (the “Company”), certain holders of the Company’s Series A Preferred Stock (“Series A Preferred”), and certain holders of the Company’s Series B Preferred Stock (“Series B Preferred”) (which parties are hereinafter collectively referred to as the “Original Parties”).

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