from 10-K 23 pages Amended and Restated Bylaws of Sgx Pharmaceuticals, Inc. Article 1 Offices Article 2 Corporate Seal

from 10-K 14 pages Change in Control Severance Agreement

from 10-K 14 pages Change in Control Severance Agreement

from 10-K 14 pages Change in Control Severance Agreement

from 10-K 14 pages Change in Control Severance Agreement

from 10-K 14 pages Change in Control Severance Agreement

from 10-K 14 pages Change in Control Severance Agreement

from 10-K 2 pages Summary of 2007 Bonus Award Program

from 10-K 2 pages 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

from 10-K 3 pages Fifth Amendment to Agreement

from 10-K 4 pages First Amendment to the Drug Discovery Agreement

from 10-K 4 pages Fourth Amendment to Lease Agreement

from 10-K 4 pages Second Amendment to Lease Agreement

from 10-K 2 pages Consent of expert or counsel

from 10-K 2 pages Management certification of annual or quarterly disclosure

from 10-K 2 pages Management certification of annual or quarterly disclosure

from 10-K 2 pages Management certification of financial report

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