EXHIBIT 10.46
FIFTH AMENDMENT TO AGREEMENT
     This Amendment to Agreement (the “Amendment”) is made and entered into
effective as of March 1, 2007 (the “Amendment Effective Date”), by and between
SGX Pharmaceuticals, Inc. (formerly known as Structural GenomiX, Inc.), a
corporation organized and existing under the laws of the State of Delaware and
having its principal place of business located at 10505 Roselle Street, San
Diego, CA 92121 (“SGX”) and Eli Lilly and Company., a corporation organized and
existing under the laws of the state of Indiana and having its principal place
of business at Lilly Corporate Center, Indianapolis, Indiana 46285, (“Lilly”).
Lilly and SGX may be referred 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 as of the Amendment Effective Date. To the extent that the
Agreement is explicitly amended by this Amendment, the terms of the Amendment
will control where the terms of the Agreement are contrary to or conflict with
the following provisions. Where the Agreement is not explicitly amended, the
terms of the Agreement will remain in force. Capitalized terms used in this
Amendment that are not defined 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 and replaced with the following:
     “From the Amendment Effective Date forward during the Term of the Research
Collaboration, SGX employees, consultants and agents involved in the
Collaboration, may not use the Lilly San Diego Facility, and the Platform and
Licensed Technology installed at the Lilly San Diego Facility to do work 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 deemed incorporated into, and governed by all other terms of, the
Agreement. The provisions of the Agreement, 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 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 in duplicate
originals by 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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