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Assignment and License Agreement [Amendment No. 1] - Cubist Pharmaceuticals Inc. and Eli Lilly and Co.

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                                                                  EXECUTION COPY

               AMENDMENT NO. 1 TO ASSIGNMENT AND LICENSE AGREEMENT

     THIS AMENDMENT NO. 1 TO ASSIGNMENT AND LICENSE AGREEMENT (this "Amendment")
dated this 1st day of July, 2003 (the "Effective Date"), is entered into between
Cubist Pharmaceuticals Incorporated, a Delaware corporation having its principal
place of business at 65 Hayden Avenue, Lexington, MA 02421 and its Affiliates
(collectively "CUBIST") and Eli Lilly and Company, an Indiana corporation having
an office and principal place of business at Lilly Corporate Center,
Indianapolis, Indiana 46285 and its Affiliates ("LILLY").

                                   WITNESSETH:

     WHEREAS, the parties entered into an ASSIGNMENT AND LICENSE AGREEMENT
effective as of October 20, 2000 (the "Agreement").

     WHEREAS, the parties have entered into a STOCK TRANSFER AGREEMENT and a
REGISTRATION RIGHTS AGREEMENT on even date herewith whereby CUBIST will transfer
to LILLY eight million dollars ($8,000,000) worth of shares of CUBIST common
stock (the "Shares") and cause such Shares to be registered under applicable
securities laws in return for a reduction of one percent (1%) on all royalties
to be paid under the Agreement.

     WHEREAS, the parties desire to amend the Agreement in accordance with
Section 17.04 thereof in certain respects as set forth below.

     NOW, THEREFORE, in consideration of the foregoing premises and the mutual
covenants set forth below, the parties amend the Agreement and agree as follows:

                                    AMENDMENT

     The Parties have reached mutual agreement that as of the Amendment
Effective Date (as defined below), each of the specific royalty rates set forth
in Sections 4.01, 4.02 and 4.03 of the Agreement, shall be deleted and shall be
replaced with a specific royalty rate that is equal to (a) the previous royalty
rate MINUS (b) one percentage point.

                            AMENDMENT EFFECTIVE DATE

     The amendments referred to above shall become effective upon the earlier
of: (a) the date on which the Registration Statement contemplated by the
REGISTRATION RIGHTS AGREEMENT shall have been declared effective by the
Securities and Exchange Commission; (b) the date on which Lilly makes its first
sale of any Shares, which date shall be provided to Cubist in writing within
five (5) days of such sale, provided that Lilly's failure to notify Cubist
thereof shall not impact the determination of the Amendment Effective Date for
purposes of this clause (b); or (c) one (1) year from the date of this Amendment
(the date on which the amendments become effective being the "Amendment
Effective Date"). In the event the Closing contemplated by the STOCK TRANSFER
AGREEMENT does not occur on July 21, 2003, this Amendment shall become null and
void.

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                                  MISCELLANEOUS

     1.1  DEFINED TERMS. All terms used, but not defined, herein shall have the
respective meanings set forth in the Agreement.

     1.2  CONTINUING EFFECT. This Amendment shall be effective for all purposes
as of the Amendment Effective Date. Except as otherwise expressly modified by
this Amendment, the Agreement shall remain in full force and effect in
accordance with its terms.

     1.3  COUNTERPARTS. This Amendment may be executed in two or more
counterparts, each of which shall be deemed an original, but all of which
together shall constitute one and the same instrument.

     IN WITNESS WHEREOF, the parties have executed this Amendment as of the date
first written above.


ELI LILLY AND COMPANY

By: /s/ Charles E. Golden
    ------------------------------------------

Name:  Charles E. Golden

Title: Executive Vice President and
       Chief Financial Officer


CUBIST PHARMACEUTICALS, INC.

By: /s/ Oliver S. Fetzer
    -------------------------------------------

Name:   Oliver S. Fetzer
      -----------------------------------------

Title:  Senior Vice President, Corporate
        Development and Chief Business Officer
       ----------------------------------------

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