0000950133-05-001884 Sample Contracts

WARRANT TO PURCHASE 10,095 SHARES OF SERIES B PREFERRED STOCK
Avalon Pharmaceuticals Inc • May 3rd, 2005 • Delaware

THIS CERTIFIES THAT, for value received, General Electric Capital Corporation (“Holder”) is entitled to subscribe for and purchase Ten Thousand Ninety Five (10,095) shares of the fully paid and nonassessable Series B Preferred Stock (the “Shares” or the “Preferred Stock”) of AVALON PHARMACEUTICALS, INC., a Delaware corporation (the “Company”), at the Warrant Price (as hereinafter defined), subject to the provisions and upon the term and conditions hereinafter set forth. As used herein, the term “Series B Preferred Stock” shall mean the Company’s presently authorized Series B Preferred Stock and any stock into which such Series B Preferred Stock may hereafter be converted or exchanged.

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Third Addendum to Consulting Agreement Dated February 1, 2000
Consulting Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

This Third Addendum is made by and between Avalon Pharmaceuticals, Inc. (formerly Therapeutic Genomics, Inc.) a Delaware corporation, located at 20358 Seneca Meadows Parkway, Germantown, MD 20876 (“AVALON”), and Bradley G. Lorimier, an individual with an address at 7807 Fox Gate Court, Bethesda, MD 20817 (“CONSULTANT”).

Avalon Pharmaceuticals Non-Qualified Stock Option Agreement
Non-Qualified Stock Option Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc
CONSULTING AGREEMENT By and Between Avalon Pharmaceuticals, Inc. and Michael Kurman Consulting
Consulting Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc • Maryland

THIS CONSULTING AGREEMENT (the “Agreement”), is made as of this 3rd day of August 2004, by Avalon Pharmaceuticals, Inc., a Delaware corporation, with its principal place of business at 20358 Seneca Meadows Parkway, Germantown, MD 20876 (“Company” or “the Company”) and Michael Kurman Consulting, located at 469 West Saddle River Road, Upper Saddle River, NJ 07458 (“Consultant” or “the Consultant”).

Therapeutic Genomics, Inc. SERIES A CONVERTIBLE PREFERRED STOCK PURCHASE AGREEMENT DECEMBER 28, 1999
Convertible Preferred Stock Purchase Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc • Delaware

Series A Convertible Preferred Stock Purchase Agreement dated as of December 28, 1999 by and between Therapeutic Genomics, Inc., a Delaware corporation (the “Company”), and those entities listed, on Schedule I attached hereto (each, individually, a “Purchaser” and collectively, the “Purchasers”).

STOCKHOLDERS’ AGREEMENT
Stockholders’ Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc • Delaware

THIS STOCKHOLDERS’ AGREEMENT (this “Agreement”) is made as of October 26, 2001 by and among Avalon Pharmaceuticals, Inc., a Delaware corporation (the “Company”), the Founding Stockholders who become parties to this Agreement by executing counterpart signature pages hereto and by authorizing the inclusion of their names on Schedule I hereto (the “Founding Stockholders”), and who are signatories to the Stockholders’ Agreement dated December 28, 1999, as amended by a certain Amendment No. 1 to Stockholders’ Agreement dated in March 2000 (the “Existing Stockholders’ Agreement”), the Series A Investors who become parties to this Agreement by executing counterpart signature pages hereto and by authorizing the inclusion of their names on Schedule II hereto, and who are signatories to the Existing Stockholders’ Agreement (the “Series A Investors”), and the Series B Investors who become parties to this Agreement by executing counterpart signature pages hereto and by authorizing the inclusion of

12,000,000 MARYLAND INDUSTRIAL DEVELOPMENT FINANCING AUTHORITY TAXABLE VARIABLE RATE DEMAND REVENUE BONDS (AVALON PHARMACEUTICALS, INC. FACILITY), SERIES 2003 INSURANCE AGREEMENT
Insurance Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc • Maryland

THIS INSURANCE AGREEMENT (this “Agreement”) is entered into as of this 1st day of April, 2003 by and between the MARYLAND INDUSTRIAL DEVELOPMENT FINANCING AUTHORITY, a body corporate and politic and a public instrumentality of the State of Maryland, in its role as insurer and not as issuer (the “Authority”), MANUFACTURERS AND TRADERS TRUST COMPANY, a New York banking corporation (the “Bank”), and AVALON PHARMACEUTICALS, INC., a Delaware corporation (the “Borrower”).

Contract
Avalon Pharmaceuticals Inc • May 3rd, 2005
REGISTRATION RIGHTS AGREEMENT
Registration Rights Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc • Delaware

This Registration Rights Agreement dated as of October 26, 2001 (the “Agreement”) by and between Avalon Pharmaceuticals, Inc., a Delaware corporation (the “Company”) and the Investors who become parties to this Agreement by executing counterpart signature pages hereto and authorizing the inclusion of their names on Schedule I hereto (the “Investors”).

LEASE
Lease Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc • Maryland

THIS LEASE AGREEMENT, made this 15th day of July, 2002, by and between WESTPHALIA CENTER II LIMITED PARTNERSHIP, a Maryland limited partnership (hereinafter referred to as “Landlord”); and, AVALON PHARMACEUTICALS, INC., a Delaware corporation, qualified to transact business and in good standing under the laws of the State of Maryland (hereinafter referred to as “Tenant”).

MASTER SECURITY AGREEMENT dated as of June 25, 2002 (“Agreement”)
Master Security Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

THIS AGREEMENT is between General Electric Capital Corporation (together with its successors and assigns, if an “Secured Party”) and Avalon Pharmaceuticals, Inc (“Debtor”). Secured Party has an office at 401 Merritt 7 Suite 23, Norwalk, CT 06851-1177. Debtor is a corporation organized and existing under the laws of the state of Delaware. Debtor’s mailing address and chief place of business is 19 Firstfield Road, Gaithersburg, MD 20878.

LICENSE, DEVELOPMENT AND COMMERCIALIZATION AGREEMENT between Vertex Pharmaceuticals Incorporated and Avalon Pharmaceuticals, Inc.
Commercialization Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc • Delaware

* The asterisk denotes that confidential portions of this exhibit have been omitted in reliance on Rule 24b-2 of the Securities Exchange Act of 1934. The confidential portions have been submitted separately to the Securities and Exchange Commission.

Amended and Restated Employment Agreement
Employment Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

This Amended and Restated Employment Agreement (this “Agreement”), on its Effective Date (as defined below), amends, restates and supercedes your prior Letter of Employment dated March 9, 2000, as amended December 2, 2002, between Avalon Pharmaceuticals, Inc., formerly Therapeutic Genomics, Inc. (the “Company”), and you (the “Prior Letter Agreement”). This Agreement shall be effective and shall supercede the Prior Letter Agreement concurrently with the effective date of the first registration statement filed by the Company to register shares of its common stock for sale to the public through one or more underwriters (the “Effective Date”). Notwithstanding the foregoing, this Agreement shall not become effective, shall be deemed null and void and shall not supercede the Prior Letter Agreement if (i) the Effective Date does not occur prior to January 1, 2006 or (ii) your employment is terminated by the Company or by you for any reason prior to the Effective Date. If this Agreement does n

Therapeutic Genomics, Inc. Amendment No. 2 to Series A Convertible Preferred Stock Purchase Agreement
Convertible Preferred Stock Purchase Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

Agreement of Amendment dated as of June 1, 2000 by and between Therapeutic Genomics, Inc., a Delaware corporation (the “Company”) and those entities listed on Schedule I hereto (the “Consenting Purchasers”).

Amended and Restated Employment Agreement
Employment Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

This Amended and Restated Employment Agreement (this “Agreement”), on its Effective Date (as defined below), amends, restates and supercedes your prior Letter of Employment dated September 28, 2001 between Avalon Pharmaceuticals, Inc. (the “Company”) and you (the “Prior Letter Agreement”). This Agreement shall be effective and shall supercede the Prior Letter Agreement concurrently with the effective date of the first registration statement filed by the Company to register shares of its common stock for sale to the public through one or more underwriters (the “Effective Date”). Notwithstanding the foregoing, this Agreement shall not become effective, shall be deemed null and void and shall not supercede the Prior Letter Agreement if (i) the Effective Date does not occur prior to January 1, 2006 or (ii) your employment is terminated by the Company or by you for any reason prior to the Effective Date. If this Agreement does not become effective, the Prior Letter Agreement shall remain in

FIRST AMENDMENT TO AVALQN PHARMACEUTICALS’ INCENTIVE STOCK OPTION AGREEMENT
Incentive Stock Option Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

This First Amendment to Avalon Pharmaceuticals, Inc. Incentive Stock Option Agreement (“First Amendment”) is dated as of January 30, 2002, by and between Avalon Pharmaceuticals, Inc., a Delaware corporation (the “Company”) and an individual whose address is set forth below the optionee signature line (the “Optionee”).

LETTER OF CREDIT AGREEMENT
Letter of Credit Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

THIS LETTER OF CREDIT AGREEMENT is dated as of April 1, 2003 and is made by and between AVALON PHARMACEUTICALS, INC., a Delaware corporation qualified to do business in the State of Maryland (the “Borrower”), and Manufacturers and Traders Trust Company, a New York banking corporation (the “Bank”).

COLLABORATION AND LICENSE AGREEMENT
Collaboration and License Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc • Delaware

Based upon this data, Aventis can advance or reject each * status. [Note: In most cases, Avalon anticipates that * across the cell line panel will define an individual * that is the likely oncogenic target for * . However, it could be possible that some * may still contain more than one * at the completion of Step C (i.e. more than * that shows correlation between DNA amplification and RNA overexpression across the cell line panel). In such cases, for * that Aventis selects for continued analysis, all * within a given * will be advanced into * and, for the purpose of calculation of the contract milestone for * , all candidate * from a given amplicon will be treated as * .]

PLEDGE AND SECURITY AGREEMENT
Pledge and Security Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc • Maryland

THIS PLEDGE AND SECURITY AGREEMENT is dated as of April 1, 2003 and is made by and between AVALON PHARMACEUTICALS, INC., a Delaware corporation qualified to do business in the State of Maryland (the “Borrower”) and MANUFACTURERS AND TRADERS TRUST COMPANY, a New York banking corporation (“M&T Bank”).

Contract
Avalon Pharmaceuticals Inc • May 3rd, 2005 • Delaware

THIS WARRANT HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED OR ANY STATE SECURITIES LAWS. NO SALE OR DISPOSITION MAY BE EFFECTED WITHOUT (i) EFFECTIVE REGISTRATION STATEMENTS RELATED THERETO, (ii)AN OPINION OF COUNSEL OR OTHER EVIDENCE, REASONABLY SATISFACTORY TO THE COMPANY, THAT SUCH REGISTRATIONS ARE NOT REQUIRED, (iii) RECEIPT OF NO-ACTION LETTERS FROM THE APPROPRIATE GOVERNMENTAL AUTHORITIES, OR (iv) OTHERWISE COMPLYING WITH THE PROVISIONS OF SECTION 7 OF THIS WARRANT.

COLLATERAL PLEDGE AND SECURITY AGREEMENT AND CONTROL AGREEMENT Among AVALON PHARMACEUTICALS, INC., as Pledgor, MANUFACTURERS AND TRADERS TRUST COMPANY, as Bank and ALLFIRST TRUST COMPANY NATIONAL ASSOCIATION as Securities Intermediary Dated as of...
Collateral Pledge and Security Agreement and Control Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc • Maryland

THIS COLLATERAL PLEDGE AND SECURITY AGREEMENT AND CONTROL AGREEMENT (this “Agreement”) is dated as of April 1, 2003 and is among AVALON PHARMACEUTICALS, INC., a Delaware corporation qualified to do business in the State of Maryland (the “Pledgor”), MANUFACTURERS AND TRADERS TRUST COMPANY, a New York banking corporation (the “Bank”), and ALLFIRST TRUST COMPANY NATIONAL ASSOCIATION (the “Securities Intermediary”).

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Amended and Restated Employment Agreement
Employment Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

This Amended and Restated Employment Agreement (this “Agreement”), on its Effective Date (as defined below), amends, restates and supercedes your prior Letter of Employment dated January 5, 2004 between Avalon Pharmaceuticals, Inc. (the “Company”) and you (the “Prior Letter Agreement”). This Agreement shall be effective and shall supercede the Prior Letter Agreement concurrently with the effective date of the first registration statement filed by the Company to register shares of its common stock for sale to the public through one or more underwriters (the “Effective Date”). Notwithstanding the foregoing, this Agreement shall not become effective, shall be deemed null and void and shall not supercede the Prior Letter Agreement if (i) the Effective Date does not occur prior to January 1, 2006 or (ii) your employment is terminated by the Company or by you for any reason prior to the Effective Date. If this Agreement does not become effective, the Prior Letter Agreement shall remain in fu

AMENDMENT NO. 1 TO STOCKHOLDERS’ AGREEMENT
Stockholders’ Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

This Amendment No. 1 (this “Amendment”), made and entered into as of April 21, 2005, amends that certain Stockholders’ Agreement, dated as of October 26, 2001 (the “Stockholders’ Agreement”) by and among Avalon Pharmaceuticals, Inc., a Delaware corporation (the “Company”), and certain stockholders of the Company as set forth therein. Capitalized terms used herein and not defined herein shall have the meanings ascribed to them in the Stockholders’ Agreement.

Amendment to CONSULTING AGREEMENT By and Between Avalon Pharmaceuticals, Inc. and William A. Scott, Ph.D.
Consulting Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

The parties hereby agree this 24th day of November , 2004 to amend the Consulting Agreement By and Between Avalon Pharmaceuticals, Inc. (“Company” or “the Company”) and William A. Scott, Ph.D. (“Consultant” or “the Consultant”) as set forth herein.

ADDENDUM TO CONSULTING AGREEMENT
Consulting Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

This document modifies the February 1, 2000 Consulting Agreement between Bradley G. Lorimier (Consultant) and Therapeutic Genomics, Inc. (TGI), to the following extent.

PLACEMENT AND REMARKETING AGREEMENT
Placement and Remarketing Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc • Maryland

THIS PLACEMENT AND REMARKETING AGREEMENT is dated as of April 1, 2003, and is made and entered into by and among MARYLAND INDUSTRIAL DEVELOPMENT FINANCING AUTHORITY, a body corporate and politic and a public instrumentality of the State of Maryland (the “Issuer”), AVALON PHARMACEUTICALS, INC., a Delaware corporation (the “Borrower”), and MANUFACTURERS AND TRADERS TRUST COMPANY, a New York banking corporation (“M&T Bank”), in its capacity as placement agent and/or remarketing agent (the “Remarketing Agent”).

Amended and Restated Employment Agreement
Employment Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

This Amended and Restated Employment Agreement (this “Agreement”), on its Effective Date (as defined below), amends, restates and supercedes your prior Letter of Employment dated January 6, 2004 between Avalon Pharmaceuticals, Inc. (the “Company”) and you (the “Prior Letter Agreement”). This Agreement shall be effective and shall supercede the Prior Letter Agreement concurrently with the effective date of the first registration statement filed by the Company to register shares of its common stock for sale to the public through one or more underwriters (the “Effective Date”). Notwithstanding the foregoing, this Agreement shall not become effective, shall be deemed null and void and shall not supercede the Prior Letter Agreement if (i) the Effective Date does not occur prior to January 1, 2006 or (ii) your employment is terminated by the Company or by you for any reason prior to the Effective Date. If this Agreement does not become effective, the Prior Letter Agreement shall remain in fu

AMENDMENT
Avalon Pharmaceuticals Inc • May 3rd, 2005

THIS AMENDMENT is made as of the 25th day of June, 2002 between General Electric Capital Corporation (“Secure Party”) and Avalon Pharmaceuticals, Inc. (“Debtor”) in connection with that certain Master Security Agreement, dated as of June 25, 2002 (“Agreement”). The terms of this Amendment are hereby incorporated into the Agreement as though fully set forth therein. Section references below refer to the section numbers of the Agreement. The Agreement is hereby amended as follows:

Amended and Restated Employment Agreement
Employment Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

This Amended and Restated Employment Agreement (this “Agreement”), on its Effective Date (as defined below), amends, restates and supercedes your prior Letter of Employment dated April 7, 2005 between Avalon Pharmaceuticals, Inc. (the “Company”) and you (the “Prior Letter Agreement”). This Agreement shall be effective and shall supercede the Prior Letter Agreement concurrently with the effective date of the first registration statement filed by the Company to register shares of its common stock for sale to the public through one or more underwriters (the “Effective Date”). Notwithstanding the foregoing, this Agreement shall not become effective, shall be deemed null and void and shall not supercede the Prior Letter Agreement if (i) the Effective Date does not occur prior to January 1, 2006 or (ii) your employment is terminated by the Company or by you for any reason prior to the Effective Date. If this Agreement does not become effective, the Prior Letter Agreement shall remain in full

LOAN AGREEMENT
Loan Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

THIS LOAN AGREEMENT is dated as of April 1, 2003, and is made by and between the MARYLAND INDUSTRIAL DEVELOPMENT FINANCING AUTHORITY, a body politic and corporate and a public instrumentality of the State of Maryland (the “Issuer”), and AVALON PHARMACEUTICALS, INC., a Delaware corporation (the “Borrower”).

CONSULTING AGREEMENT By and Between Avalon Pharmaceuticals, Inc. and William A. Scott, Ph.D.
Consulting Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc • Maryland

THIS CONSULTING AGREEMENT (the “Agreement”), is made as of this 4th day of August 2004 (the “Effective Date”), by Avalon Pharmaceuticals, Inc., a Delaware corporation, with its principal place of business at 20358 Seneca Meadows Parkway, Germantown, MD 20876 (“Company” or “the Company”) and William A. Scott, Ph.D., with an address of 1021 Creamery Road, Newtown, PA 18940 (the “Consultant”), and supersedes the February 28, 2003 Consulting Agreement between Company and Consultant.

Therapeutic Genomics, Inc. Amendment No. 1 to Series A Convertible Preferred Stock Purchase Agreement
Convertible Preferred Stock Purchase Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

Agreement of Amendment dated as of March 1, 2000 by and between Therapeutic Genomics, Inc., a Delaware corporation (the “Company”) and those entities listed on Schedule I hereto (the “Initial Purchasers”).

SECOND AMENDMENT TO AVALON PHARMACEUTICALS’ INCENTIVE STOCK OPTION AGREEMENT
Incentive Stock Option Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

This Second Amendment to Avalon Pharmaceuticals, Inc. Incentive Stock Option Agreement (“Second Amendment”) is dated as of _____________, 2003, by and between Avalon Pharmaceuticals, Inc., a Delaware corporation (the “Company”) and an individual whose address is set forth below the optionee signature line (the “Optionee”).

Amended and Restated Employment Agreement
Employment Agreement • May 3rd, 2005 • Avalon Pharmaceuticals Inc

This Amended and Restated Employment Agreement (this “Agreement”), on its Effective Date (as defined below), amends, restates and supercedes your prior Letter of Employment dated December 2, 1999, as amended December 3, 2002, between Avalon Pharmaceuticals, Inc., formerly Therapeutic Genomics, Inc. (the “Company”), and you (the “Prior Letter Agreement”). This Agreement shall be effective and shall supercede the Prior Letter Agreement concurrently with the effective date of the first registration statement filed by the Company to register shares of its common stock for sale to the public through one or more underwriters (the “Effective Date”). Notwithstanding the foregoing, this Agreement shall not become effective, shall be deemed null and void and shall not supercede the Prior Letter Agreement if (i) the Effective Date does not occur prior to January 1, 2006 or (ii) your employment is terminated by the Company or by you for any reason prior to the Effective Date. If this Agreement doe

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