Document:

exv10w44

 

EXHIBIT
10.44

Summary of 2007 Bonus Award Program

The bonus award program provides that the Company must meet at least 50% of its overall corporate
goals for the year (as determined by our Board of Directors) for any bonus compensation to be paid
and that executive officers and employees must be rated as an “Achieves expected levels of
performance” or higher in their annual performance review in order to be eligible for a bonus
payout. The ratings and bonus opportunity as a percentage of base salary for the executive
officers are listed in the table below.

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	Achieves	 	Exceeds	 	Consistently	 	Significantly
	 	 	Expected	 	Expected	 	Exceeds	 	Exceeds
	 	 	Levels of	 	Levels of	 	Expected Levels	 	Expected Levels
	Performance Ratings	 	Performance	 	Performance	 	of Performance	 	of Performance
	 
	VP (Executive Officer),
Chief Financial Officer
	 	20%	 	 	25	%	 	 	30	%	 	 	35	%
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Chief Scientific Officer
	 	25%	 	 	30	%	 	 	35	%	 	 	40	%
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Chief Executive Officer
	 	30%	 	 	35	%	 	 	45	%	 	 	50	%

For the 2007 bonus plan, our Board of Directors has established certain strategic and
financial objectives for the Company, directed at progressing certain of our kinase inhibitor
research programs towards clinical development, entering into a significant strategic transaction
and achieving specific financial objectives. The goals for bonuses have been established so that
target attainment is not assured and attainment will require a high level of persistence, effort
and execution on the part of our executive officers. Even if the requisite strategic and financial
objectives are satisfied, our Compensation Committee has full discretion to determine the actual
amount, if any, of the bonus awarded to any individual under our bonus award program.

4exv10w45

 

EXHIBIT
10.45

February 9, 2007

Dr. Stephen K. Burley

c/o SGX Pharmaceuticals, Inc.

10505 Roselle Street

San Diego, CA 92121

Dear Stephen:

As discussed, I confirm the agreement of the Compensation Committee of the Board to award you a
cash bonus of $250,000, contingent and effective upon, and to be paid to you, subject to your
continued employment with SGX upon, the closing prior to December 31, 2007 of a corporate
transaction with aggregate proceeds to SGX or SGX’s security holders of at least $50 million. For
purposes of this cash bonus award, aggregate proceeds from a corporate transaction would include
upfront payments, the cash amount paid to purchase any of SGX’s equity securities, committed
funding over the initial term (if a collaboration), and potential milestone payments or other
contingent payments achievable within 12 months, as determined by SGX’s board of directors. If the
aggregate proceeds include proceeds in the form of securities, the securities would be valued at
the listed market value of the securities if the securities are listed on a securities exchange, or
the value determined by SGX’s board of directors if the securities are not listed on a securities
exchange.

To confirm your agreement to the above, please sign where indicated below.

Sincerely,

/s/ Mike Grey

Mike Grey

President and Chief Executive Officer

Agreed this 9th day of February, 2007

/s/
Stephen K. Burley          

Dr. Stephen K. Burley

SGX
Pharmaceuticals, Inc. • www.sgxpharma.com

Corporate Headquarters • 10505 Roselle Street • San Diego, CA 92121 • 858.558.4850 • 858.558.4859 fax

SGX Beamline • Argonne National Laboratory, Bldg. 438A • 9700 S. Cass Avenue • Argonne, IL 60439 • 630.252.0820 • 630.252.0835 faxexv10w46

 

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.”

-1-

 

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	 	 
	 

	 	 	 	 	 	 

-2-exv10w47

 

EXHIBIT
10.47

FIRST AMENDMENT TO THE DRUG DISCOVERY AGREEMENT

     This First Amendment is entered into by and between SGX Pharmaceuticals, Inc., (formerly known
as Structural GenomiX, Inc.) (“SGX”) and Cystic Fibrosis Foundation Therapeutics, Inc. (“CFFT”) and
is effective as of March 1, 2007 (“Amendment Effective Date”). Collectively, SGX and CFFT are
referred to hereinafter as the “Parties”.

     WHEREAS, the Parties entered into the Drug Discovery Agreement dated as of January 1, 2005
(the “DDA”); and

     WHEREAS, the Parties wish to amend the DDA in the manner hereinafter provided; and

     WHEREAS, except for this First Amendment, the DDA shall be otherwise unchanged and remain in
full force and effect.

     NOW THEREFORE, the Parties agree as follows:

     1. Deletion of Section 7.1. Section 7.1 is hereby deleted and after the effective
date of this First Amendment, numbered Section 7.1 shall be intentionally omitted.

     2. Without Cause Termination. Section 7.2 shall be amended to read as follows:

          “7.2 Without Cause Termination. CFFT may terminate this Agreement upon
sixty (60) days notice to SGX. In the event of such termination, no further amount
shall be payable by CFFT to SGX except for any outstanding accrued liabilities
existing as of the effective date of termination.”

 

 

     3. Corresponding Amendments.

          a. Section 2.25 shall be amended by deleting the word “Hits”.

          b. The last sentence of Section 3.5(b) shall be deleted.

          c. Subparagraph (b) of Section 4.1 shall be deleted and replaced with the following:
“(b) an exclusive (even as to SGX) worldwide, sublicensable, perpetual license in
the Structure Data (other than Hits, an Early Lead Series and Lead Series) in the
Field under all of its rights and interests and (c) a non-exclusive, worldwide,
sublicensable, perpetual license in the Hits identified in Appendix F to this
Agreement, in the Field.”

          d. The Appendix F attached hereto will be added to the Agreement.

     IN WITNESS WHEREOF, the Parties have executed this First Amendment as of the Amendment
Effective Date.

SGX PHARMACEUTICALS, INC.

	 	 	 	 	 
	By:

	 	/s/ Todd Myers	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	Title:
	 	CFO	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	Date:
	 	2/12/07	 	 
	 

	 	 	 	 

CYSTIC FIBROSIS FOUNDATION THERAPEUTICS, INC.

	 	 	 	 	 
	By:

	 	/s/ Robert J. Beall	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	Title:
	 	President and CEO	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	Date:
	 	2/2/07	 	 
	 

	 	 	 	 
	 
	 	 	 	 

-2-

 

APPENDIX F

Hits:

FAST Fragments = 67978, 66336, 67171, 66199, 67153, 66326 (67153 analog), 68097, 66299, 12970

Commercial Analogs = 71516, 71515, 71764, 72056 (12970 analog)

Synthesized Analogs

Parent: 12970     Analog: 72664

Parent: 71516     Analog: 72316

Parent: 67153     Analog: 72512

Parent: 67153     Analog: 72530

Parent: 67153     Analog: 72536

Parent: 67153     Analog: 72547

Parent: 67153     Analog: 72554

Parent: 67153     Analog: 72558

Parent: 67153     Analog: 73166

Parent: 67153     Analog: 73181

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