3 Dimensional Pharmaceuticals Inc Sample Contracts

3 Dimensional Pharmaceuticals Inc – EXECUTION COPY STOCKHOLDER AGREEMENT dated as of January 15, 2003, (this "Agreement"), among JOHNSON & JOHNSON, a New Jersey corporation ("Parent"), and the individuals and other parties listed on Schedule A attached hereto (each, a "Stockholder" and, collectively, the "Stockholders"). WHEREAS Parent, Longbow Merger Sub, Inc., a Delaware corporation and a wholly owned Subsidiary of Parent ("Sub"), and 3-Dimensional Pharmaceuticals, Inc., a Delaware corporation (the "Company"), propose to enter into an Agreement and Plan of Merger dated as of the date hereof (as the same may be amended or suppl (January 17th, 2003)
3 Dimensional Pharmaceuticals Inc – Contract (July 28th, 2000)

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3 Dimensional Pharmaceuticals Inc – NINTH RESTATED CERTIFICATE OF INCORPORATION OF 3-DIMENSIONAL PHARMACEUTICALS, INC. 3-DIMENSIONAL PHARMACEUTICALS, INC. (the "Corporation"), a corporation organized and existing under and by virtue of the General Corporation Law of the State of Delaware, does hereby certify as follows: 1. The name of the Corporation is 3-Dimensional Pharmaceuticals, Inc. The Certificate of Incorporation of the Corporation was originally filed by the Corporation with the Secretary of State of the State of Delaware on March 11, 1993, a Certificate of Amendment to the Certificate of Incorporation was filed by the (July 28th, 2000)
3 Dimensional Pharmaceuticals Inc – AMENDED AND RESTATED BYLAWS OF 3-DIMENSIONAL PHARMACEUTICALS, INC. Incorporated under the Laws of the State of Delaware ARTICLE I OFFICES AND RECORDS Section 1.1 Delaware Office. The principal office of the Corporation in the State of Delaware shall be located in the City of Wilmington, County of New Castle, and the name and address of its registered agent is The Corporation Trust Company, Corporation Trust Center, 1209 Orange Street, Wilmington, Delaware. Section 1.2 Other Offices. The Corporation may have such other offices, either within or without the State of Delaware, as the Board of Dir (July 28th, 2000)
3 Dimensional Pharmaceuticals Inc – EIGHTH RESTATED CERTIFICATE OF INCORPORATION OF 3-DIMENSIONAL PHARMACEUTICALS, INC. 3-DIMENSIONAL PHARMACEUTICALS, INC. (the "Corporation"), a corporation organized and existing under and by virtue of the General Corporation Law of the State of Delaware (the "General Corporation Law"), hereby certifies as follows: FIRST: The name of the Corporation is 3-Dimensional Pharmaceuticals, Inc. The Certificate of Incorporation of the Corporation was originally filed by the Corporation with the Secretary of State of the State of Delaware on March 11, 1993, a Certificate of Amendment to the Certificate (July 28th, 2000)
3 Dimensional Pharmaceuticals Inc – -ii- AMENDED AND RESTATED LEASE -------------------------- LEASE made this ____ day of __________________, 1997 between Eagleview TECHNOLOGY PARTNERS, a limited partnership, successor in interest to the Hankin Group ("Landlord"), with its office at 717 Constitution Drive, P.O. Box "562, Exton, PA 19341 AND 3-DIMENSIONAL PHARMACEUTICALS, INC., a Delaware corporation ("Tenant"), with its office at 665 Stockton Drive, Suite 104, Exton, PA 19341 BACKGROUND The Hankin Group, predecessor in interest to the Landlord, and Tenant entered into a Lease on April 28, 1994 for 15,861 square feet of space (" (July 28th, 2000)
3 Dimensional Pharmaceuticals Inc – _________ SHARES OF COMMON STOCK 3 - DIMENSIONAL PHARMACEUTICALS, INC. UNDERWRITING AGREEMENT ---------------------- ______, 2000 BEAR, STEARNS & CO. INC. U.S. BANCORP PIPER JAFFRAY INC. CHASE SECURITIES INC. as Representatives of the several Underwriters named in Schedule I attached hereto c/o Bear, Stearns & Co. Inc. 245 Park Avenue New York, NY 10167 Ladies and Gentlemen: 3-Dimensional Pharmaceuticals, Inc., a corporation organized and existing under the laws of Delaware (the "Company"), proposes, subject to the terms and conditions stated herein, to issue and sell to the several underwrite (July 28th, 2000)
3 Dimensional Pharmaceuticals Inc – Lessee hereby irrevocably authorizes Lessor to insert in this Schedule the Commencement Date and the due date of the first rental payment. Except as expressly provided or modified hereby, all the terms and provisions of the Master Lease Agreement shall remain in full force and effect. The Purchase Date shall be June 1, 2001. The Stipulated Loss Value of any items of Equipment shall be an amount equal to the present value of all future Rent discounted at a rate of 8% per annum plus the Reversionary Value. The Reversionary Value of any item of Equipment shall be 10% of Equipment Cost. TRANSAMERI (July 13th, 2000)

--------------------------------------------------------------------------------------------------------- QTY EQUIPMENT PURCHASE INVOICE NO. CATALOG SERIAL NO. DESCRIPTION ORDER NO. --------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------- 1 Vacuum Desiccaator Cabiner 970235 278404021597 8644 N/A --------------------------------------------------------------------------------------------------------- 970235 Total --------------------------------------------------------------------------------------------------------- -----------------------------------------

3 Dimensional Pharmaceuticals Inc – Equipment Location (if other than above address of Borrower): n/a --- Lender and Borrower have entered into a Master Loan and Security Agreement No. 7110 dated June 18, 1998 (the "Master Loan Agreement") which is incorporated herein and this is a Schedule to the Master Loan Agreement. All words and terms used herein and not specifically defined herein shall have the same meanings as set forth in the Master Loan Agreement. 1. THE LOAN AND LOAN REPAYMENT. As requested by Borrower and pursuant to the Master Loan Agreement, Lender agrees to lend to Borrower the sum of one --- million six hundred f (July 13th, 2000)

EXHIBIT A EQUIPMENT SCHEDULE 3-DIMENSIONAL PHARM -------------------------------------------------------------------------------------------------------------------------- 3-Dimensional Pharmaceuticals, Inc. 665 Stockton Drive, Suite 104 Equip Location Exton, PA 19341 -------------------------------------------------------------------------------------------------------------------------- Supplier Description Qty Serial No. Price Extended Sub-Total Price -------------------------------------------------------------------------------------------------------------------------- Advanced Chemtech 1 lock, ASM, 96 Well H/C Rv, Tfe 1 97176 5,500.00 5,500.00

3 Dimensional Pharmaceuticals Inc – WARRANT TO PURCHASE COMMON STOCK (May 23rd, 2000)
3 Dimensional Pharmaceuticals Inc – COLLABORATIVE DISCOVERY AND LEAD OPTIMIZATION AGREEMENT (May 23rd, 2000)
3 Dimensional Pharmaceuticals Inc – RESEARCH AND LICENSE AGREEMENT (May 23rd, 2000)
3 Dimensional Pharmaceuticals Inc – WARRANT TO PURCHASE COMMON STOCK (May 23rd, 2000)
3 Dimensional Pharmaceuticals Inc – COLLABORATIVE RESEARCH AND LICENSE AGREEMENT (May 23rd, 2000)
3 Dimensional Pharmaceuticals Inc – WARRANT TO PURCHASE COMMON STOCK (May 23rd, 2000)
3 Dimensional Pharmaceuticals Inc – WARRANT TO PURCHASE COMMON STOCK (May 23rd, 2000)
3 Dimensional Pharmaceuticals Inc – WARRANT TO PURCHASE COMMON STOCK (May 23rd, 2000)
3 Dimensional Pharmaceuticals Inc – RESEARCH COLLABORATION AGREEMENT (May 23rd, 2000)
3 Dimensional Pharmaceuticals Inc – WARRANT TO PURCHASE COMMON STOCK (May 23rd, 2000)
3 Dimensional Pharmaceuticals Inc – THIRD AMENDED AND RESTATED STOCKHOLDERS' AGREEMENT (May 23rd, 2000)
3 Dimensional Pharmaceuticals Inc – SETTLEMENT AGREEMENT (May 23rd, 2000)
3 Dimensional Pharmaceuticals Inc – SERIES C PREFERRED STOCK PURCHASE AGREEMENT (May 23rd, 2000)
3 Dimensional Pharmaceuticals Inc – SERIES B PREFERRED STOCK PURCHASE AGREEMENT (May 23rd, 2000)
3 Dimensional Pharmaceuticals Inc – WARRANT TO PURCHASE COMMON STOCK (May 23rd, 2000)
3 Dimensional Pharmaceuticals Inc – WARRANT TO PURCHASE COMMON STOCK (May 23rd, 2000)