0001193125-06-070902 Sample Contracts

THIS WARRANT AND THE SHARES OF COMMON STOCK ISSUED UPON ITS EXERCISE ARE SUBJECT TO THE RESTRICTIONS ON TRANSFER SET FORTH IN SECTION 5 OF THIS WARRANT
Achillion Pharmaceuticals Inc • March 31st, 2006 • Connecticut

Achillion Pharmaceuticals, Inc., a Delaware corporation (the “Company”), for value received, hereby certifies that [name] or its registered assigns (the “Registered Holder”), is entitled, subject to the terms and conditions set forth below, to purchase from the Company, at any time or from time to time on or after the Initial Exercise Date (as defined below) and on or before 5:00 p.m. (Eastern Standard Time) on October 28, 2009 that number of shares of Common Stock, $.001 par value per share, of the Company (the “Common Stock”) as is determined by application of the formula set forth below.

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EMPLOYMENT AGREEMENT
Employment Agreement • March 31st, 2006 • Achillion Pharmaceuticals Inc • Connecticut

THIS EMPLOYMENT AGREEMENT (the “Agreement”), effective as of the 26th day of May 2004, is entered into by Achillion Pharmaceuticals, Inc., a Delaware corporation with its principal place of business at 300 George Street, New Haven, CT 06511-6624 (the “Company”), and Gautam Shah, Ph.D., residing at 6 Todd’s Way, Westport, CT 06880 (the “Employee”).

Confidential Materials omitted and filed separately with the Securities and Exchange Commission. Asterisks denote omissions. RESEARCH COLLABORATION AND LICENSE AGREEMENT
Research Collaboration and License Agreement • March 31st, 2006 • Achillion Pharmaceuticals Inc • New York

THIS RESEARCH COLLABORATION AND LICENSE AGREEMENT (“Agreement”) is made effective as of November 24, 2004 (“Effective Date”) by and between ACHILLION PHARMACEUTICALS, INC., a Delaware corporation (“Achillion”), with its principal place of business at 300 George Street, New Haven, Connecticut 06511, USA, and GILEAD SCIENCES, INC., a Delaware corporation (“Gilead”), with its principal place of business at 333 Lakeside Drive, Foster City, California 94404, USA. Achillion and Gilead are sometimes referred to in this Agreement individually as a “Party” and collectively as the “Parties”.

SECOND AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT
Investor Rights Agreement • March 31st, 2006 • Achillion Pharmaceuticals Inc • Delaware

This Second Amended and Restated Investor Rights Agreement is made as of November 17, 2005 by and among Achillion Pharmaceuticals, Inc., a Delaware corporation (the “Company”), the holders of shares of the Company’s Series A Convertible Preferred Stock, $.01 par value per share (the “Series A Preferred”), Series B Convertible Preferred Stock, $.01 par value per share (the “Series B Preferred”), Series C Convertible Preferred Stock, $.01 par value per share (the “Series C Preferred”), Series C-1 Convertible Preferred Stock, $.01 par value per share (the “Series C-1 Preferred”), and Series C-2 Convertible Preferred Stock, $.01 par value per share (the “Series C-2 Preferred”) (collectively, the “Holders”).

Confidential Materials omitted and filed separately with the Securities and Exchange Commission. Asterisks denote omissions. LICENSE AGREEMENT
License Agreement • March 31st, 2006 • Achillion Pharmaceuticals Inc • Connecticut

WHEREAS, pursuant to the terms of a certain License Agreement, dated as of August 31, 1994, as amended, by and between Yale University (“Yale”) and Licensor (the “Yale License Agreement”), Yale has licensed to Licensor certain inventions relating to, among other things, potential anti-viral compounds, including ß-L-FD4C;

Confidential Materials omitted and filed separately with the Securities and Exchange Commission. Asterisks denote omissions. LICENSE AGREEMENT by and between ACHILLION PHARMACEUTICALS, INC. and THE UNIVERSITY OF MARYLAND, BALTIMORE COUNTY
License Agreement • March 31st, 2006 • Achillion Pharmaceuticals Inc • Maryland

This agreement (the “Agreement”), dated the 15th day of November, 2002 (the “Effective Date”), is by and between Achillion Pharmaceuticals, Inc. , a corporation organized and existing under the laws of the State of Delaware (“ACHILLION”), and The University of Maryland, Baltimore County, a constituent institution of the University System of Maryland, which is an agency of the State of Maryland (“UMBC”).

MASTER SECURITY AGREEMENT dated as of January 24, 2002 (“Agreement”)
Master Security Agreement • March 31st, 2006 • Achillion Pharmaceuticals Inc • Connecticut

THIS AGREEMENT is between General Electric Capital Corporation (together with its successors and assigns, if any, “Secured Party”) and Achillion Pharmaceuticals, Inc. (“Debtor”). Secured Party has an office at 401 Merritt 7 Suite 23, Norwalk, CT 06851. 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 300 George Street, New Haven, CT 06511.

EMPLOYMENT AGREEMENT
Employment Agreement • March 31st, 2006 • Achillion Pharmaceuticals Inc • Connecticut

THIS EMPLOYMENT AGREEMENT (the “Agreement”), effective as of the 19th day of July 2004, is entered into by Achillion Pharmaceuticals, Inc., a Delaware corporation with its principal place of business at 300 George Street, New Haven, CT 06511-6624 (the “Company”), and Michael D. Kishbauch., residing at 18 Cherryville Road, Flemington, NJ (the “Employee”).

ACHILLION PHARMACEUTICALS, INC Nonstatutory Stock Option Agreement Granted Under 1998 Stock Option Plan
Stock Option Agreement • March 31st, 2006 • Achillion Pharmaceuticals Inc
MASTER SECURITY AGREEMENT dated as of December 30, 2005 (“Agreement”)
Master Security Agreement • March 31st, 2006 • Achillion Pharmaceuticals Inc • Connecticut

THIS AGREEMENT is between Oxford Finance Corporation (together with its successors and assigns, if any, “Secured Party”) and Achillion Pharmaceuticals, Inc. (“Debtor”). Secured Party has an office at 133 N. Fairfax Street, Alexandria, VA 22314. 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 300 George Street, New Haven, CT 06511.

Confidential Materials omitted and filed separately with the Securities and Exchange Commission. Asterisks denote omissions. LICENSE AGREEMENT BETWEEN ACHILLION PHARMACEUTICALS, INC. AND EMORY UNIVERSITY EFFECTIVE AS OF JULY 19, 2002
License Agreement • March 31st, 2006 • Achillion Pharmaceuticals Inc • New York

This License Agreement (this “Agreement”) is made by and between Emory University, a Georgia non-profit corporation, with offices located at 1380 South Oxford Road, N.E., Atlanta, GA 30322 (“Emory”), and Achillion Pharmaceuticals, Inc., a Delaware corporation, with its principal offices at 300 George Street, New Haven, CT 06511 (“Achillion”). The Agreement is effective as of July 19, 2002 (the “Effective Date”).

THIRD AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT
Stockholders’ Agreement • March 31st, 2006 • Achillion Pharmaceuticals Inc • Delaware

This Third Amended and Restated Stockholders’ Agreement is made as of the 17th day of November, 2005 by and among ACHILLION PHARMACEUTICALS, INC., a Delaware corporation (the “Company”), certain holders of Common Stock (as defined below) listed as Founders on the signature pages hereto (the “Founders”), the individuals listed as Common Stockholders on the signature pages hereto (the “Common Stockholders”), the individuals and entities listed as Investors on the signature pages hereto (collectively, the “Investors”, and, together with the Founders and the Common Stockholders, the “Stockholders”).

NEITHER THIS WARRANT NOR THE SECURITIES ISSUABLE UPON EXERCISE OF THIS WARRANT HAVE BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED. NO SALE OR DISPOSITION MAY BE EFFECTED EXCEPT IN COMPLIANCE WITH RULE 144 UNDER SAID ACT OR WITHOUT AN...
Achillion Pharmaceuticals Inc • March 31st, 2006 • Connecticut

THIS CERTIFIES THAT, for value received, General Electric Capital Corporation (“Holder”) is entitled to subscribe for and purchase up to Eighty Three Thousand Three Hundred Thirty Three (83,333) shares of the fully paid and nonassessable Series C-2 Convertible Preferred Stock (the “Shares” or the “Series C-2 Preferred Stock”) of Achillion Pharmaceuticals, Inc., a Delaware corporation (the “Company”), at the Warrant Price (as hereinafter defined), subject to the provisions and upon the terms and conditions hereinafter set forth. As used herein, the term “Series C-2 Preferred Stock” shall mean the Company’s presently authorized Series C-2 Preferred Stock and any stock into which such Series C-2 Preferred Stock may hereafter be converted or exchanged.

MASTER SECURITY AGREEMENT dated as of May 15, 2003 (“Agreement”)
Master Security Agreement • March 31st, 2006 • Achillion Pharmaceuticals Inc

THIS AGREEMENT is between Webster Bank (together with its successors and assigns, if any, “Secured Party”) and Achillion Pharmaceuticals, Inc. (“Debtor”). Secured Party has an office at 80 Elm Street, New Haven, CT 06510. 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 300 George Street, New Haven, CT 06511.

LOAN AGREEMENT by and between CONNECTICUT INNOVATIONS, INCORPORATED and ACHILLION PHARMACEUTICALS, INC. March 30,2001
Loan Agreement • March 31st, 2006 • Achillion Pharmaceuticals Inc • Connecticut

This LOAN AGREEMENT (the “Agreement”) is made as of this 30th day of March, 2001 by and between CONNECTICUT INNOVATIONS, INCORPORATED, with an office and place of business located at 999 West Street, Rocky Hill, Connecticut 06067 (“CII”) and ACHILLION PHARMACEUTICALS, INC., a Delaware Corporation, with its chief executive office located at 300 George Street, New Haven, Connecticut (the “Borrower”).

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