Document:

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                                                                    EXHIBIT 10.8

                                                                  DR. TIM HARRIS

November 12, 2004

CONFIDENTIAL

Alex Barkas, Ph.D.
Chairman of the Compensation Committee
Structural GenomiX, Inc.
10505 Roselle Street
San Diego, CA 92121

   RE:  SEPARATION OF EMPLOYMENT OF SGX CEO DR. TIMOTHY HARRIS

Dear Alex,

This letter reflects the agreements we have reached regarding the termination of
my employment with SGX and our respective obligations under my Executive
Employment Agreement with the Company dated May 2001 (the "Employment
Agreement"). This letter modifies the Employment Agreement as set forth below.

     1. SEPARATION OF EMPLOYMENT FROM SGX

     My employment with the Company will terminate on December 31st 2004 or any
earlier date that I accept full time employment with another company. I will
also resign from the Board of Directors on that date.

     2. SEVERANCE COMPENSATION TO COMMENCE JANUARY 1, 2005

     SGX's contractual obligations based on termination without cause are
currently governed by my Employment Agreement. Pursuant to subparagraph 7.2 of
the Agreement, SGX is obligated to pay me my current base salary of $351,520.00
per year for a 12 month period following termination, and also to pay any and
all Standard Entitlements (as defined in the Employment Agreement), including
incentive pay, cash bonuses and/or stock options as defined by subparagraphs
4.2, 4.3 and 4.4 and 7.1 of the Agreement upon termination of my employment. It
is my understanding that a proportionate bonus will be owed to me if the SGX
Board of Directors determines, in its sole discretion, that the Company's 2004
bonus goals have been reached, and/or if other members of senior staff receive
bonus payments for 2004. This will be paid to me on the same schedule as if I
had still been in employment. Severance compensation shall commence on January
1, 2005 and continue until December 31, 2005. This

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severance compensation is guaranteed until June 30th 2005. Thereafter, it will
continue on a month to month basis until December 31st 2005 only if I am not in
full-time employment or substantial equivalent elsewhere. If full time
employment is accepted before January 1st 2005 then the six month severance will
start from the date that the full time employment is accepted.

     I will continue to be bound by the provisions of the Employment Agreement
which specifically survive the termination of my employment as set forth in
Section 16.7 of the Employment Agreement. In addition, as contemplated by
Section 7.2 of the Employment Agreement, the severance compensation and other
benefits set forth in this letter are conditioned upon my execution of the full
general release contemplated by Section 7.2(b) on my last day of employment.

     3. HEALTH INSURANCE-COBRA - PAYMENT FOR 18 MONTHS

     If I am eligible under the applicable plans, SGX shall be responsible for
continuing to provide my existing health insurance benefits for 18 months. In
the event of my non-eligibility, SGX shall agree to pay the monthly cost of
COBRA commencing on January 1, 2005 for a period of eighteen (18) months unless
I begin full time employment elsewhere.

     4. STOCK OPTIONS TO VEST IMMEDIATELY WITH 5 YEAR EXERCISE TERM

     Any unvested stock options grants that I currently hold shall fully vest on
or before December 31, 2004 when I leave full time employment at SGX. I have
65,584 unvested shares (at $0.85/share) based on the 6/5/03 stock option grant
(# 434) that under my proposal would vest in this way. The aforementioned
options and an additional 43,940 vested options (at $0.25/share) pursuant to the
grant dated 1/1/04 (#458) shall be exercisable over five (5) years from January
1st 2005.

     5. NEW STOCK OPTION GRANT REPRESENTING 1% OF TOTAL OUTSTANDING EQUITY POST
FINANCING

     Within six months of closing the next equity financing or concomitantly
with the issue of stock options to senior management of the Company, the Company
will issue a stock option grant or warrant to me (at a price to be determined)
representing 1% of the fully diluted total outstanding equity. This stock option
grant will be fully vested and have a five year exercise term from date of
issue.

     6. REIMBURSEMENT OF EXPENSES INCURRED ON CANCELLED SHARES

On December 18, 2001 the Company issued me a 100,000 share stock option grant
(at $0.85 per share). The grant (#334) was subsequently cancelled by the Company
but not until after I had exercised the options. This cost me $5446.84 in
interest expenses. The Company has agreed to

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pay me a (one time grossed up) payment of $7394.09 due December 31st 2004 to
cover this cost.

     7. CONSULTANT TO THE COMPANY

     I am available to act as a consultant to the Company for 60 days post
termination as stated in the Employment Agreement (see Section 7.2c)

Alex, I hope that this accurately reflects our conversation of November 4th
2004. In order to make sure that there are no misunderstandings it would be
helpful if you could sign this letter below and return a copy to me so that the
company can take the necessary steps to put the agreement in place.

It has been a pleasure working with you all and I hope we will be able to do so
again in the future.

Very Truly Yours,

/s/ Tim Harris                                     /s/ Alex Barkas
Tim Harris                                         ----------------------------
CEO SGX                                            Signed & Agreed:  Alex Barkas
                                                   Chairman, SGX Comp Committee

cc:     Fred Muto (Cooley-Godward)

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                         EXECUTIVE EMPLOYMENT AGREEMENT

     This Executive Employment Agreement ("Agreement") is effective as of May 1,
2001 ("Effective Date"), by and between Structural GenomiX, Inc., with its
principal place of business at 10505 Roselle Street, San Diego, California 92121
(the "SGX"), a Delaware corporation, and Dr. Tim Harris, who resides at ________
___________________________________ ("Executive").

     The parties agree as follows:

     1. Employment. SGX hereby employs Executive, and Executive hereby accepts
such employment, upon the terms and conditions set forth herein.

     2. Duties.

          2.1. Position. Executive is employed in the position of Chief
Executive Officer and President reporting to the company's Board of Directors,
and shall have the duties and responsibilities assigned by SGX. Executive is
responsible for setting and ensuring that the strategic and financial position
of SGX is achieved; and overseeing all business and science related concerns of
SGX. Executive shall perform faithfully and diligently such duties, as well as
such other duties as SGX shall reasonably assign from time to time. SGX reserves
the right to modify Executive's position and duties at any time in its sole and
reasonable discretion.

          2.2. Best Efforts/Full-time. Executive will expend Executive's best
efforts on behalf of SGX, and will abide by all policies and decisions made by
SGX, as well as all applicable federal, state and local laws, regulations or
ordinances. Executive will act in the best interest of SGX at all times.
Executive shall devote Executive's full business time and efforts to the
performance of Executive's assigned duties, unless Executive notifies SGX in
advance of Executive's intent to engage in other paid work and receives SGX'
express written consent to do so. Executive must not engage in any work, paid or
unpaid, that creates an actual or potential conflict of interest with SGX. If
SGX believes a conflict exists, SGX may ask Executive to choose whether to
discontinue the other work or resign employment with SGX.

          2.3. Board Seat; Performance Expectations. Executive will continue to
have a seat on the Board of Directors of the Company.

          2.3. Work Location. Executive's principal place of work shall be
located in San Diego, California, at SGX' offices.

     3. Term. The employment relationship pursuant to this Agreement shall be
for an initial term commencing on the Effective Date set forth above and
continue until properly terminated in accordance with Section 7 below.

     4. Compensation.

          4.1. Salary. As compensation for the proper and satisfactory
performance of all duties to be performed by Executive hereunder, SGX shall pay
to Executive a Base Salary of Three Hundred Twenty Five Thousand Dollars
($325,000.00) per year, payable in accordance with the normal payroll practices
of SGX, less required deductions for state and federal withholding tax, social
security and all other employment taxes and payroll deductions. In the event
Executive's employment under this Agreement is terminated by either party, for
any reason, Executive will be entitled to receive the Base Salary prorated to
the date of termination.

          4.2. Incentive Compensation. Executive will be eligible to receive
incentive compensation. If SGX, in its sole and absolute discretion, grants
executive incentive compensation, the terms, amount and payment of such, if any,
will be determined solely by SGX.

          4.3. Stock Options. Executive may be granted stock options from time
to time in the discretion of SGX subject to the terms and conditions of SGX'
2000 Equity Incentive Plan (the "Incentive Plan") and the Company's form of
stock option agreement. Executive's present stock options and vesting schedule
are set forth in Exhibit A to this Agreement and incorporated herein.

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          4.4. Cash Bonus Program. As President and CEO, Executive is eligible
to earn a cash bonus equal to 40% of Executive's base salary, or $130,000,
provided Executive meets the eligibility requirements and performance objectives
set forth in SGX' bonus program, which are determined in SGX' sole discretion.

          4.5. Performance and Salary Review. SGX will periodically review
Executive's performance on no less than an annual basis. Executive's salary
and/or other compensation will be reviewed yearly and may be adjusted from time
to time in SGX' sole and absolute discretion.

     5. Customary Fringe Benefits. Executive will be eligible for all customary
and usual fringe benefits generally available to executives of SGX subject to
the terms and conditions of SGX' benefit plan documents. SGX reserves the right
to modify or eliminate the fringe benefits on a prospective basis, at any time,
effective upon notice to Executive.

     6. Business Expenses. Executive will be reimbursed for all out-of-pocket
business expenses reasonably incurred in the performance of Executive's duties
on behalf of SGX. To obtain reimbursement, expenses must be submitted promptly
with appropriate supporting documentation in accordance with SGX' policies.

     7. Termination of Employment.

          7.1. Termination for Cause by SGX. Although SGX anticipates a mutually
rewarding employment relationship with Executive, SGX may terminate Executive's
employment immediately at any time for cause. Cause includes, but is not limited
to, one or more of the following: (a) acts or omissions deemed by SGX to
constitute gross negligence, recklessness, willful misconduct or dishonesty on
the part of Executive with respect to Executive's obligations under this
Agreement or otherwise relating to the business of SGX; (b) Executive's willful,
material breach of this Agreement; (c) Executive's conviction or entry of a plea
of guilty or nolo contendere for fraud, misappropriation or embezzlement, or of
any felony; or engaging in any conduct which SGX, in its discretion, determines
has or may adversely impact SGX. (d) Executive's material breach of fiduciary
duty toward SGX; (e) Executive's material breach of any element of SGX'
Confidential Information and Invention Assignment Agreement, including without
limitation, Executive's theft, dilution, or other misappropriation or careless
treatment of SGX' proprietary information; (f) Executive's inability to perform
all of the essential functions and duties of Executive's position, with or
without reasonable accommodation other than for reason of temporary illness; or
(g) Executive's death. In the event Executive's employment is terminated in
accordance with this subparagraph 7.1, Executive shall be entitled to receive
only the Base Salary then in effect, prorated to the date of termination, and
any benefits, including any benefits under the bonus program and Incentive Plan,
and expense reimbursements to which Executive is entitled by virtue of his prior
employment with SGX (collectively referred to as "Standard Entitlements."). All
other SGX obligations to Executive pursuant to this Agreement will become
automatically terminated and completely extinguished. Executive will not be
entitled to receive the Severance Payment or any part thereof described in
subparagraph 7.2 below.

          7.2. Termination Without Cause By SGX/Severance. SGX may terminate
Executive's employment under this Agreement without cause at any time on thirty
(30) days' advance written notice to Executive. In the event of such
termination, Executive will receive the Standard Entitlements, plus a severance
payment equivalent to twelve months of Executive's Base Salary then in effect on
the date of termination (the "Severance Payment") payable in accordance with
SGX' regular payroll cycle, and the vesting of any outstanding stock options
will be accelerated by twenty-four (24) months, provided that Executive: (a)
complies with all surviving provisions of this Agreement as specified in
subparagraph 16.7 below, (b) executes a full general release, releasing all
claims, known or unknown, that Executive may have against SGX arising out of or
any way related to Executive's employment or termination of employment with SGX;
and (c) agrees to act as a consultant for SGX for up to a maximum of sixty (60)
days, without additional compensation, if requested to do so by SGX. All other
SGX obligations to Executive pursuant to this Agreement will become
automatically terminated and completely extinguished.

          7.3. Voluntary Resignation By Executive. Executive may voluntarily
resign Executive's position with SGX at any time on thirty (30) days advance
written notice. In the event of Executive's resignation, Executive shall be
entitled to receive only the Base Salary then in effect, prorated to the date of
resignation, and the Standard Entitlements. In addition, Executive's stock
options, existing as of the date of resignation, will continue to vest as
scheduled pursuant to

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the Incentive Plan for sixty (60) days. All other SGX obligations to Executive
pursuant to this Agreement will become automatically terminated and completely
extinguished. In addition, Executive will not be entitled to receive the
Severance Payment described in paragraph 7.2 above.

          7.4. Termination of Executive Following Change In Control.

               (a) Severance Payment. If Executive's employment is terminated by
SGX without cause within one year after a Change of Control (as that term is
defined below), Executive shall be entitled to receive the Standard
Entitlements, plus the Severance Payment described in subparagraph 7.2 above,
and that the vesting of any outstanding stock options will be accelerated by 24
months, provided Executive complies with the conditions in subparagraph 7.2
above. For the purpose of this section, termination without cause shall include
acts by SGX which substantially change all of Executive's duties and
responsibilities which existed prior to the Change in Control. All other SGX
obligations to Executive pursuant to this Agreement will become automatically
terminated and completely extinguished.

               (b) 280G. If, due to the benefits provided under subparagraph
7.4(a) above, Executive is subject to any excise tax due to characterization of
any amounts payable under subparagraph 7.4(a) as excess parachute payments
pursuant to Section 4999 of the Internal Revenue Code of 1986, as amended (the
"Code"), Executive may elect, in Executive's sole discretion, to reduce the
amounts payable under subparagraph 7.4(a) in order to avoid any "excess
parachute payment" under Section 280G(b)(l) of the Code.

               (c) Change of Control. A Change of Control is defined as 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.

     8. Competitive Employment. During the term of Executive's employment with
SGX and during any period in which Executive is receiving payments (other than
any dividend s on stock) from SGX or acting as a consultant with or without
payment, Executive agrees that Executive will not directly or indirectly compete
with SGX in any way, and will not act as an officer, director, executive,
consultant, shareholder (other than stock of publicly held companies),
volunteer, lender, or agent of any business enterprise of the same nature as, or
which is in competition with, the business in which SGX is now engaged or in
which SGX becomes engaged during the term of Executive's employment with SGX, as
may be determined by SGX in its sole discretion. Further, Executive agrees not
to refer any client or potential client to competitors of SGX without SGX'
written consent during the term of Executive's employment with SGX or during any
period in which Executive is receiving payments (other than any dividends on
stock) from SGX or acting as a consultant with or without payment.

     9. Confidentiality and Proprietary Rights. Executive agrees to abide by
SGX' Proprietary Rights policies and to protect the intellectual property of
SGX. In accordance, Executive has signed, contemporaneously with the execution
of this Agreement, a Confidential Information and Invention Assignment
Agreement, which is incorporated herein by this reference.

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     10. Non-Solicitation.

          10.1. Non-Solicitation of Employees and Independent Contractors.
Executive agrees that during Executive's employment with SGX and for a period of
one year after the termination of Executive's employment with SGX, Executive
will not directly or indirectly, separately or in association with others,
interfere with, impair, disrupt or damage SGX' relationship with any employee or
independent contractor; solicit, encourage or attempt to hire any of SGX'
employees or independent contractors; or cause others to solicit or encourage
any of SGX' employees or independent contractors to discontinue their employment
or services with SGX.

          10.2. Non-Solicitation of Customers. Executive acknowledges that
proprietary information about SGX' customers is confidential and constitutes
trade secrets of SGX. Executive agrees that during Executive's employment with
SGX and for a period of one year following the termination of Executive's
employment with SGX, Executive will not, either directly or indirectly,
separately or in association with others, do any of the following: (i) make
known, to any person, firm or corporation, the names and addresses of any of the
customers of SGX or contacts of SGX within the biotechnology industry or any
other information pertaining to such persons; (ii) call on, solicit, take away,
or attempt to call on, solicit or take away any of the customers of SGX on whom
Executive called or with whom Executive became aware or acquainted during
Executive's association with SGX, whether for Executive or for any other person,
firm or corporation; or (iii) use or make known to any person or entity, the
strategies, tactics, practices, and procedures by which SGX does business.

     11. Injunctive Relief. Executive acknowledges that Executive's breach of
the covenants contained in paragraphs 8-10 (collectively "Covenants") would
cause irreparable injury to SGX and agrees that in the event of any such breach,
SGX shall be entitled to seek temporary, preliminary and permanent injunctive
relief without the necessity of proving actual damages or posting any bond or
other security.

     12. Accounting and Indemnification. In the event Executive breaches any of
the Covenants contained in paragraphs 8-10, SGX shall have the right and remedy
to require Executive to: (a) account for and pay over to SGX all compensation,
profits, monies, accruals, increments or other benefits derived or received by
Executive or any associated party deriving such benefits as a result of any such
breach of the Covenants; and (b) to indemnify SGX against any other losses,
damages (including special and consequential damages), costs and expenses,
including actual attorneys' fees and court costs, which may be incurred by them
and which result from or arise out of any such breach or threatened breach of
the Covenants. Both parties agree that the provisions of this paragraph 12 will
not adequately compensate SGX for SGX' injury in the event of Executive's breach
of any of the Covenants. Accordingly, the parties agree the provisions of this
paragraph 12 will not in any way limit or interfere with SGX' right to seek
injunctive relief under paragraph 11.

     13. Return of SGX Property. On termination of employment with SGX for
whatever reason, or at the request of SGX before termination, Executive agrees
to promptly deliver to SGX all records, files, computer disks, memoranda,
documents, lists and other information regarding or containing any Proprietary
Information (as defined in the Confidential Information and Invention Assignment
Agreement executed herewith), including all copies, reproductions, summaries or
excerpts thereof, then in Executive's possession or control, whether prepared by
Executive or others. Executive also agrees to promptly return, upon termination
or at any time upon SGX' request, any and all SGX property issued to Executive,
including but not limited to computers, facsimile transmission equipment,
cellular phones, keys and credits cards. Executive further agrees that should
Executive discover any SGX property or Proprietary Information in Executive's
possession after Executive's termination and departure from SGX, Executive
agrees to return it promptly to SGX without retaining copies or excerpts of any
kind.

     14. No Violation of Rights of Third Parties. Executive warrants that
Executive's performance of all the terms of this Agreement does not and will not
breach any agreement to keep in confidence proprietary information, knowledge or
data acquired by Executive prior to Executive's employment with SGX. Executive
agrees not to disclose to SGX, or induce SGX to use, any confidential or
proprietary information or material belonging to any previous employers or
others. Executive warrants that Executive is not a party to any other agreement
that will interfere with Executive's full compliance with this Agreement.
Executive further agrees not to enter into any agreement, whether written or
oral, in conflict with the provisions of this Agreement.

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     15. Agreement to Arbitrate. Executive and SGX agree to arbitrate any
controversy, claim or dispute between them arising out of or in any way related
to this Agreement, the employment relationship between them, and any disputes
upon termination of employment, except as provided in subparagraph 15.1 below,
to the fullest extent permitted by law. This method of resolving disputes shall
be the sole and exclusive remedy of the parties. Accordingly, the parties
understand that, except as provided in this paragraph 15 or as otherwise
required by law, they are giving up their rights to have their disputes decided
in a court of law and, if applicable, by a jury, and instead agree that their
disputes shall be decided by arbitration.

          15.1. Scope of the Agreement. The disputes subject to this agreement
to arbitrate include all potential claims between Executive and SGX relating to
employment, such as breach of contract, tort, discrimination, harassment,
wrongful termination, demotion, discipline, failure to accommodate, family and
medical leave, compensation or benefits claims, constitutional claims and claims
for violation of any local, state or federal law, statute, regulation or
ordinance or common law to the fullest extent permitted by law. Claims for
workers' compensation or unemployment insurance benefits, if any, and SGX' right
to obtain injunctive relief pursuant to paragraph 11 above are excluded. For the
purposes of this agreement to arbitrate, references to "SGX" include SGX and all
subsidiary and related entities and their employees, supervisors, officers,
directors, owners, agents, benefit plans, benefit plan sponsors, fiduciaries,
administrators, affiliates and all successors and assigns of any of them, and
this agreement to arbitrate shall apply to them to the extent Executive's claims
arise out of or relate to their actions on behalf of SGX.

          15.2. Initiation of Arbitration. Either party may exercise the right
to arbitrate by providing the other party with written notice of any and all
claims forming the basis of such right in sufficient detail to inform the other
party of the substance of such claims.

          15.3. Arbitration Procedure. The arbitration will be conducted in
accordance with the then current rules for resolution of employment disputes of
the American Arbitration Association ("AAA") at its offices in San Diego,
California. If the parties cannot agree on the single neutral arbitrator, such
arbitrator shall be selected in accordance with the AAA rules. The parties are
entitled to representation by an attorney or other representative of their
choosing. The parties will also be permitted to conduct discovery sufficient to
present their respective cases. The arbitrator will be required to issue a
written arbitration decision that will reveal the essential findings and
conclusions on which an award is based, and shall have the power to enter any
award that could be entered by a judge of the Superior Court of the State of
California, and only such power, and shall follow the law. In the event the
arbitrator does not follow the law, the arbitrator will have exceeded the scope
of his or her authority and the parties may, at their option, file a motion to
vacate the award in court. Otherwise, the parties agree to abide by and perform
any award rendered by the arbitrator. Judgment on the award may be entered in
any court having jurisdiction thereof.

     16. General Provisions.

          16.1. Successors and Assigns. The rights and obligations of SGX under
this Agreement shall inure to the benefit of and shall be binding upon the
successors and assigns of SGX. Executive shall not be entitled to assign any of
Executive's rights or obligations under this Agreement.

          16.2. Waiver. Either party's failure to enforce any provision of this
Agreement shall not in any way be construed as a waiver of any such provision,
or prevent that party thereafter from enforcing each and every other provision
of this Agreement.

          16.3. Severability. In the event any provision of this Agreement is
found to be unenforceable by an arbitrator or court of competent jurisdiction,
such provision shall be deemed modified to the extent necessary to allow
enforceability of the provision as so limited, it being intended that the
parties shall receive the benefit contemplated herein to the fullest extent
permitted by law. If a deemed modification is not satisfactory in the judgment
of such arbitrator or court, the unenforceable provision shall be deemed
deleted, and the validity and enforceability of the remaining provisions shall
not be affected thereby.

          16.4. Interpretation; Construction. The headings set forth in this
Agreement are for convenience only and shall not be used in interpreting this
Agreement. This Agreement has been drafted by legal counsel representing SGX,
but Executive has participated in the negotiation of its terms. Furthermore,
Executive acknowledges that Executive

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has had an opportunity to review and revise the Agreement and have it reviewed
by legal counsel, if desired, and, therefore, the normal rule of construction to
the effect that any ambiguities are to be resolved against the drafting party
shall not be employed in the interpretation of this Agreement.

          16.5. Governing Law. This Agreement will be governed by and construed
in accordance with the laws of the United States and the State of California.
Each party consents to the jurisdiction and venue of the state or federal courts
in the State where Executive is employed, in any action, suit, or proceeding
arising out of or relating to this Agreement.

          16.6. Notices. Any notice required or permitted by this Agreement
shall be in writing and shall be delivered as follows with notice deemed given
as indicated: (a) by personal delivery when delivered personally; (b) by
overnight courier upon written verification of receipt; (c) by telecopy or
facsimile transmission upon acknowledgment of receipt of electronic
transmission; or (d) by certified or registered mail, return receipt requested,
upon verification of receipt. Notice shall be sent to the addresses set forth
below, or such other address as either party may specify in writing.

          16.7. Survival. Paragraphs 8 ("Competitive Employment"), 9
("Confidentiality and Proprietary Rights"), 10 ("Non-Solicitation"), 11
("Injunctive Relief"), 12 ("Accounting and Indemnification"), 13 ("Return of SGX
Property") 15 ("Agreement to Arbitrate"), 16 ("General Provisions") and 17
("Entire Agreement") of this Agreement shall survive Executive's employment by
SGX.

     17. Entire Agreement. This Agreement, including SGX' Incentive Plan, Bonus
Plan and Confidential Information and Invention Assignment Agreement herein
incorporated by reference, constitutes the entire agreement between the parties
relating to this subject matter and supersedes all prior or simultaneous
representations, discussions, negotiations, and agreements, whether written or
oral. This Agreement may be amended or modified only with the written consent of
Executive and the Board of Directors of SGX. No oral waiver, amendment or
modification will be effective under any circumstances whatsoever.

THE PARTIES TO THIS AGREEMENT HAVE READ THE FOREGOING AGREEMENT AND FULLY
UNDERSTAND EACH AND EVERY PROVISION CONTAINED HEREIN. WHEREFORE, THE PARTIES
HAVE EXECUTED THIS AGREEMENT ON THE DATES SHOWN BELOW.

                                                            Executive
Dated:  August ____, 2001
                                                ________________________________
                                                Dr. Tim Harris

                                                Structural GenomiX Inc.

Dated:  August ____, 2001                       By:_____________________________

                                                      Its:______________________

                                     Page 6<PAGE>

[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

<PAGE>

[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

<PAGE>

[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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