[SGX LOGO]

                                                                    EXHIBIT 10.9

June 3, 2005

                                                                    CONFIDENTIAL

Mr. James A. Rotherham


Dear James:

I am pleased to offer you the position of Chief Financial Officer with
Structural GenomiX, Inc. ("SGX" or the "Company") reporting to Mike Grey,
President & CEO. This position is categorized as full-time regular exempt.
Following are the details of our offer.

      -     The salary in this position is $235,000 on an annualized basis, or
            approximately $9,038.46 bi-weekly, subject to standard deductions
            and withholdings.

      -     Subject to approval by the Board of Directors (the "Board"), you
            will receive an option to purchase 190,000 shares of the Company's
            common stock at a price per share equal to its fair market value as
            determined by the Board. This option will have a vesting
            commencement date of your first day of employment with the Company.
            Twenty five percent (25%) of the granted shares will vest on the
            first anniversary of the vesting commencement date. The remaining
            options vest monthly thereafter until the fourth anniversary of the
            vesting commencement date. The offer of these shares is conditioned
            upon your acceptance of our offer of employment and subject to the
            terms and requirements of the Company's 2000 Equity Incentive Plan
            (the "Incentive Plan") and the Company's form of stock option
            agreement.

      -     You are also eligible to participate in the Company's cash bonus
            program. In your position, you are eligible to earn a cash bonus up
            to 40% of your base salary. In order to be eligible to receive this
            bonus, you must satisfy the eligibility requirements outlined in the
            Company's bonus program, including accomplishing the performance
            objectives set for your position. Participants in the bonus program
            who are employed for part of a calendar year will be eligible to
            receive a pro-rated bonus for that first partial year of employment.
            Employees hired in the fourth quarter of a calendar year are
            eligible to participate in the bonus program in the following year.

      -     Included in the compensation package is a benefits plan that offers
            medical, dental, vision, life insurance, Accidental Death and
            Dismemberment. (AD&D) insurance, long-term disability, short-term
            disability insurance; and a 401(k) plan. For full-time employees,
            vacation accrues on a pay period basis at the annual rate of 120
            hours (three weeks). The vacation accrual increases by one day after
            each anniversary with the Company, up to a maximum of 20 days per
            year. The Company also provides employees with five days of sick
            time per year.

As a condition of your employment, you will be required to sign a copy of our
Employment, Confidential Information and Invention Assignment Agreement, which
is attached for your information. In addition, to conform with the Immigration
Reform and Control Act of 1986, please bring with you on your start date the
original of one of the documents noted in List A on the I-9 form attached or one
document from List B and one document from List C. If you do not have the
originals of any of these documents, please call me immediately. Please do not
complete or sign the I-9 until you begin employment. This offer is contingent
upon your providing sufficient documentation to show proof of eligibility for
employment in the United States.

                   STRUCTURAL GENOMIX, INC. - WWW.STROMIX.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 fax



[SGX LOGO]

James A. Rotherham
Page 2 of 3

      It is the Company's policy to fully respect the proprietary and
      confidential information rights of your previous employers. You are not
      expected to disclose, nor are you allowed to use for the Company's
      purposes, any confidential or proprietary information you may have
      acquired as a result of previous employment.

      Your employment with the company is not for a specified term, but may be
      terminated by you or the company at any time, with or without cause. The
      nature of your employment as set forth in this paragraph cannot be
      modified in any way except by written agreement signed by you and an
      officer of SGX.

      In the event of a Change of Control (as that term is defined below) the
      vesting of any outstanding stock options described above will be
      accelerated by 12 months. In the event your employment is terminated by
      the Company without cause within one year after a Change of Control, the
      vesting of your outstanding stock options described above will be
      accelerated by a further 12 months, provided that you comply with all
      surviving provisions of this letter and the Employment, Confidential
      Information and Invention Assignment Agreement Agreement and execute a
      full general release, releasing all claims, known or unknown, that you may
      have against the Company arising out of or any way related to you
      employment or termination of employment with the Company. In the event of
      such termination all other obligations of the Company to you pursuant to
      this letter will become automatically terminated and completely
      extinguished.

      A Change of Control means any one of the following occurrences:

            (i) Any "person" (as such term is used in Sections 13(d) and 14(d)
      of the Securities Exchange Act of 1934 (the "Exchange Act"), other than a
      trustee or other fiduciary holding securities of SGX under an employee
      benefit plan of SGX, becomes the "beneficial owner" (as defined in Rule
      13d-3 promulgated under the Exchange Act), directly or indirectly, of the
      securities of SGX representing more than 50% of (a) the outstanding shares
      of common stock of SGX or (b) the combined voting power of SGX'
      then-outstanding securities; or

            (ii) The sale or disposition of all or substantially all of SGX'
      assets (or any transaction having similar effect is consummated) other
      than to an entity of which SGX owns at least 50% of the Voting Stock so
      long as the sale or disposition is not under duress of SGX' financial
      hardship; or

            (iii) SGX is party to a merger or consolidation that results in the
      holders of voting securities of SGX outstanding immediately prior thereto
      failing to continue to represent (either by remaining outstanding or by
      being converted into voting securities of the surviving entity) less than
      50% of the combined voting power of the voting securities of SGX or such
      surviving entity outstanding immediately after such merger or
      consolidation.

      I am pleased to extend this offer to you and look forward to your
      acceptance. Please sign and return the attached copy of this offer letter
      as soon as possible, but within at least five days of receipt, to indicate
      your agreement with the terms of this offer. Once signed by you, this
      letter and the Employment, Confidential Information and Invention
      Assignment Agreement will constitute the complete agreement between you
      and Structural GenomiX, Inc. regarding employment matters and will
      supersede all prior written or oral agreements or understandings on these
      matters. This letter may only be modified by a written agreement signed by
      you and an officer of SGX. We hope you will join us June 20, 2005 or
      sooner. Please contact me if you have any questions.

      I feel you will be able to make an immediate contribution to our efforts,
      and I think you will enjoy the rewards of working for an innovative,
      fast-paced organization.

      Sincerely,

      /s/ Mike Grey
      ---------------------

      Mike Grey
      President & CEO



[SGX LOGO]

James A. Rotherham
Page 3 of 3

Attachments:

      -     Copy of Offer Letter

      -     I-9

      -     Employment, Confidential Information And Invention Assignment
            Agreement

I accept the terms of employment as described in this offer letter and will
start my employment on 6/13/05.

Signature: /s/ James A. Rotherham                     Date: 6/12/05
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