EXHIBIT10.46**FIFTH AMENDMENT TO AGREEMENT**     **This Amendment to Agreement**(the “Amendment”) is made and entered into effective asof March 1, 2007 (the “Amendment Effective Date”), by and between **SGX Pharmaceuticals, Inc.**(formerly known as Structural GenomiX, Inc.)**,**a corporation organized and existingunder the laws of the State of Delaware and having its principal place of business located at 10505Roselle Street, San Diego, CA 92121 (“SGX”) and **Eli Lilly and Company.,** a corporationorganized and existing under the laws of the state of Indiana and having its principal place ofbusiness at Lilly Corporate Center, Indianapolis, Indiana 46285, (“Lilly”). Lilly and SGX may bereferred to herein as a “Party” or, collectively, as “Parties”.**Recitals**     **A. **Lilly and SGX have entered into a Collaboration and License Agreement effective April 14,2003, as amended July 1, 2003, January 30, 2004, November 11, 2004, and March 31, 2005 (the“Agreement”), under which the Parties have agreed to conduct a collaborative research program.     **B. **The Parties desire to amend the terms of the Agreement as provided in this Amendment.     **Now, Therefore,** the Parties agree as follows:**1.****Amendment of the Agreement**     The Parties hereby agree to amend the terms of the Agreement as provided below, effective asof the Amendment Effective Date. To the extent that the Agreement is explicitly amended by thisAmendment, the terms of the Amendment will control where the terms of the Agreement are contrary toor conflict with the following provisions. Where the Agreement is not explicitly amended, theterms of the Agreement will remain in force. Capitalized terms used in this Amendment that are notdefined herein shall have the same meanings as such terms are defined in the Agreement.     **1.1 Amend Section 3.****2(b)****.**Section 3.2(b) of the Agreement is hereby deleted in its entirety.     **1.2 Amend Section 3.9**. Section 3.9(a) of the Agreement is hereby deleted in its entirety andreplaced with the following:     “From the Amendment Effective Date forward during the Term of the Research Collaboration, SGXemployees, consultants and agents involved in the Collaboration, may not use the Lilly San DiegoFacility, and the Platform and Licensed Technology installed at the Lilly San Diego Facility to dowork under this Agreement, unless given written permission by Lilly.”
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**2.****Miscellaneous**     **2.1 Full Force and Effect.**This Amendment amends the terms of the Agreement and is deemedincorporated into, and governed by all other terms of, the Agreement. The provisions of theAgreement, as amended by this Amendment, remain in full force and effect.     **2.2 Counterparts.**This Amendment may be executed in two or more counterparts, each of whichshall be deemed an original, but all of which together shall constitute one and the sameinstrument.     **In Witness Whereof,**the Parties have executed this Amendment in duplicate originalsby their authorized officers as of the date and year first above written.         **Eli Lilly and Company**         By: /s/ William W. Chin                  Title: Vice President, Discovery Research                  **SGX Pharmaceuticals, Inc.**         By: /s/ Todd Myers            Title: CFO         
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