Document:

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                                                                 EXHIBIT 10.20

                                           *** TEXT OMITTED AND FILED SEPARATELY
                                    PURSUANT TO A CONFIDENTIAL TREATMENT REQUEST
                                            UNDER 17 C.F.R. SECTION 200.80(b)(4)
                                               AND RULE 406 UNDER THE SECURITIES
                                                         ACT OF 1933, AS AMENDED

                             AMENDMENT TO AGREEMENT

         THIS AMENDMENT TO AGREEMENT (the "Amendment") is made and entered into
effective as of November 11, 2004 (the "Amendment Effective Date"), by and
between 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 and January 30, 2004
(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 otherwise defined herein shall have the same
meanings as such terms are defined in the Agreement.

         1.1 AMEND SECTION 4.1. Section 4.1 of the Agreement is hereby amended
to delete subsection (c) in its entirety and replace it with the following: "(c)
(i) Within forty-five (45) days after the Amendment Effective Date, Lilly will
pay SGX a non-refundable research fee of $2,500,000, provided however, that SGX
has committed a total of [...***...] ([...***...]) [...***...] to the Research
Collaboration during the period between March 26, 2003 and the Amendment
Effective Date; and (ii) within forty-five (45) days after the second
anniversary of the Effective Date, Lilly will pay SGX a non-refundable research
fee of $[...***...], provided however, that SGX has committed a total of
[...***...] ([...***...]) [...***...] to the Research Collaboration during the
period between March 26, 2003 and the [...***...] of the Effective Date. If SGX
has not honored such [...***...] ([...***...]) [...***...] commitment, then
Lilly will pay SGX a pro-rated amount under sub-paragraph (ii) above,
proportionate with the amount of FTEs that have actually been used as long as
the total number of FTEs committed by SGX during the period between March 26,
2003 and the second anniversary of the Effective Date exceeds [...***...]."

                                       1.   ***CONFIDENTIAL TREATMENT REQUESTED

<PAGE>

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/ [illegible]
                                 -------------------------------------

                             Title: VP, DCRT
                                    ----------------------------------

                             STRUCTURAL GENOMIX, INC.

                             By: /s/ Herbert G. Mutter
                                 -------------------------------------

                             Title: Vice President, Finance
                                    ----------------------------------

                                       2.<PAGE>

                                                                 EXHIBIT 10.21

                                           *** TEXT OMITTED AND FILED SEPARATELY
                                    PURSUANT TO A CONFIDENTIAL TREATMENT REQUEST
                                            UNDER 17 C.F.R. SECTION 200.80(b)(4)
                                               AND RULE 406 UNDER THE SECURITIES
                                                         ACT OF 1933, AS AMENDED

                             AMENDMENT TO AGREEMENT

         THIS AMENDMENT TO AGREEMENT (the "Amendment") is made and entered into
effective as of March 31st, 2005 (the "Amendment Effective Date"), by and
between 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
and November 11, 2004 (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 1.43. Section 1.43 of the Agreement is hereby deleted
in its entirety and replaced with the following: "Term of the Research
Collaboration" means the period commencing on the Effective Date and terminating
on the fifth anniversary of the Effective Date.

         1.2 AMEND SECTION 2.6. Section 2.6 of the Agreement is hereby amended
by inserting in the second line, after "[...***...] ([...***...]) [...***...],"
the following: "per year of Term of the Research Collaboration."

         1.3 AMEND SECTION 2.10. Section 2.10 of the Agreement is hereby amended
by deleting in the second line "second anniversary of the Effective Date" and
substituting therefor the following: "end of the Term of the Research
Collaboration."

         1.4 AMEND SECTION 3.4. Section 3.4(b) of the Agreement is hereby
amended by deleting in the second line "completion of the Initial Training," and
substituting therefor the

                                       1.   ***CONFIDENTIAL TREATMENT REQUESTED

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following: "the Term of the Research Collaboration," and in the third sentence
thereof by deleting "payment by Lilly pursuant lo Section 4.2(d)," and
substituting therefor the following: "determination by Lilly that the Phase II
Acceptance Criteria have been met."

         1.5 AMEND SECTION 3.5. Section 3.5(ii) of the Agreement is hereby
amended by inserting in front of "maintain" in the first line, the following:
"at Lilly's expense, make best efforts to conclude within three (3) months of
the Amendment Effective Date and"; and by deleting "Term of the Technology
Collaboration" and substituting therefor the following: "Term of the Research
Collaboration."

         1.6 AMEND SECTION 3.6(a). Section 3.6(a) of the Agreement is hereby
amended by deleting the last sentence and replacing it with the following: "In
the event that Lilly desires to obtain a license to any SGX Additional
Technology, Lilly will provide SGX with written notice of such desire to SGX
within thirty days of such identification by SGX and upon receipt of written
notice by SGX the Parties will negotiate in good faith the appropriate license
fee to be paid by Lilly to SGX for such SGX Additional Technology. In the event
that the Parties agree such amount, then upon payment by Lilly to SGX of such
amount, such SGX Additional Technology will be deemed to be Licensed Technology
and SGX will have the obligation to provide Lilly with support under the terms
of Sections 3.4(b) and (c) for such SGX Additional Technology (other than SGX
Research Stage Technology)."

         1.7 AMEND SECTION 3.9. Section 3.9(a) of the Agreement is hereby
deleted in its entirety and replaced with the following:

         "During the Term of the Research Collaboration, SGX employees,
consultants and agents involved in the Collaboration, may use the Lilly San
Diego Facility, and the Platform and Licensed Technology installed at the Lilly
San Diego Facility only to do work under this Agreement, unless given written
permission by Lilly. SGX will ensure that commencing on April 14, 2005 and
continuing throughout the remainder of the Term of the Research Collaboration, a
minimum of [...***...] will perform Research Plan activities in the Lilly San
Diego Facility."

         1.8 AMEND SECTION 4.1. Section 4.1 of the Agreement is hereby amended
as follows:

         (a) a new Section 4.1(d) is inserted as follows: "(d) Within thirty
(30) days after the second anniversary of the Effective Date, Lilly will pay to
SGX a non-refundable research fee of [...***...] US dollars ($[...***...]) in
consideration of which SGX hereby grants to Lilly a non-exclusive,
sub-licensable and perpetual license to SOPS for protein production generated
hereunder.

         (b) a new Section 4.1(e) is inserted as follows: "(e) Commencing on the
second anniversary of the Effective Date, Lilly will pay SGX research funding
for [...***...] ([...***...]) FTEs per year during the Term of the Research
Collaboration. For each such FTE, Lilly will pay SGX at an annualized rate of
[...***...] ($[...***...]) per FTE per year, which rate shall increase annually
beginning on the third anniversary of the Effective Date, to reflect any
increase in the CPI, using 2005 as the base year, up to a maximum of a
[...***...] percent ([...***...]%)

                                       2.   ***CONFIDENTIAL TREATMENT REQUESTED

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increase annually. The amounts to be paid under this Section 4.1(e) shall be
paid quarterly in advance on the basis that there will be [...***...]
([...***...]) FTEs involved in the Research Collaboration in each twelve (12)
month period following the second anniversary of the Effective Date (each such
twelve (12) month period a "Collaboration Year"). The initial payment under this
Section 4.1(e) will be made within thirty (30) days of the second anniversary of
the Effective Date and subsequent payments will be made on or before July 14,
October 14, and January 14 during the Term of the Research Collaboration. Within
sixty (60) days following the end of each Collaboration Year, SGX will provide
Lilly with an accounting of the actual number of FTEs engaged in the Research
Collaboration during the previous Collaboration Year and will accord Lilly a
credit (or in the case of the last annual accounting, a refund) for any
deficiency in FTEs engaged in the Research Collaboration from the number of
[...***...] ([...***...])."

         1.9 AMEND SECTION 5.5(a). Section 5.5(a) of the Agreement is hereby
amended by inserting after the penultimate sentence the following:
"Notwithstanding the foregoing, if the combined number of Collaboration Targets
for which Target Structure has not yet been obtained and Crystallizable Proteins
is greater than [...***...] ([...***...]) at any given time, then this Section
5.5(a) shall not apply to Crystallizable Proteins in the amount greater than
[...***...] ([...***...]), as Lilly shall designate".

         1.10 AMEND SECTION 10.6. Section 10.6 of the Agreement is hereby
amended by deleting the words "Sections 4.1(b) and (c) from subsection (ii) and
replacing them with: "Sections 4.1(b), (c) and (e)".

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.

                                       3.   ***CONFIDENTIAL TREATMENT REQUESTED

<PAGE>

         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/ Steven M. Paul
                                   ---------------------------------------------

                               Title:  Executive Vice President, Science and
                                       Technology
                                       -----------------------------------------

                               STRUCTURAL GENOMIX, INC.

                               By: /s/ M. Grey
                                   ---------------------------------------------

                               Title: President and CEO
                                      ------------------------------------------

                                       4.

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