Document:

<PAGE>   1
                                                                    EXHIBIT 10.4

                       AMENDMENT NO. 3 TO VOTING AGREEMENT

        THIS AMENDMENT NO. 3 TO VOTING AGREEMENT ("Amendment") is made as of
April 28, 2000, by and among Discovery Partners International, Inc., a
California corporation formerly known as IRORI (the "Company"), Enterprise
Partners III, L.P., Enterprise Partners III Associates, L.P. (together,
"Enterprise"), Mayfield VIII, Mayfield Associates Fund II (together,
"Mayfield"), Crosspoint Venture Partners-1996, Crosspoint Venture Partners
LS-1997 (together, "Crosspoint"), Agilent Technologies, Inc. (formerly
Hewlett-Packard Company) ("Agilent"), Pacific Venture Group II, L.P.
("Pacific"), BayStar Capital, L.P. and BayStar International Ltd. (together
"BayStar"), Hayden J. Trubitt ("Trubitt") and Axys Pharmaceuticals, Inc.
("Axys"), with reference to the Voting Agreement, as amended and restated by
Amendment No. 2 to the Voting Agreement, dated April 7, 2000 (the "Voting
Agreement"), among the Company, Enterprise, Mayfield, Crosspoint, Agilent,
Pacific, Baystar and Trubitt. Enterprise, Mayfield, Crosspoint, Agilent,
Pacific, Baystar and Trubitt are collectively referred to herein as the
"Investors." RECITALS

        A. The Company, DPII Newco, LLC, a Delaware limited liability company
("Merger Sub"), Axys and Axys Advanced Technologies, Inc., a Delaware
corporation ("AAT"), have entered into that certain Agreement and Plan of
Merger, dated as of April 11, 2000 (the "Merger Agreement") pursuant to which
Merger Sub is being merged with and into AAT with the consequence that AAT will
become a wholly-owned subsidiary of the Company.

        B. Pursuant to the Company's Restated Articles of Incorporation, as
amended, the holders of the Company's Preferred Stock ("Preferred Stock") are
entitled to elect five (5) directors of the Company (the "Preferred Directors").

        C. This Amendment is entered into as a condition to and in consideration
of the Merger Agreement.

        NOW, THEREFORE, IT IS HEREBY AGREED THAT THE VOTING AGREEMENT IS AMENDED
AND RESTATED TO READ IN FULL AS FOLLOWS:

        1.     Agreement to Vote for Enterprise Nominee.

               a. During the term of this Voting Agreement, each of the
Investors agrees to vote all of its shares of the Company's Series A Preferred
Stock ("Series A Shares"), Series B Preferred Stock ("Series B Shares"), Series
C Preferred Stock ("Series C Shares"), Series D Preferred Stock ("Series D
Shares") and Series E Preferred Stock ("Series E Shares") now or hereafter owned
by it to elect one (1) nominee of Enterprise (the "Enterprise Nominee") as a
Preferred Director.

<PAGE>   2
               b. Prior to each election of directors of the Company, Enterprise
shall designate the Enterprise Nominee in writing to the Company. The Company
shall promptly notify each of the Investors of Enterprise's choice of such
nominee. Any vacancy occurring because of the death, resignation, removal or
disqualification of the Enterprise Nominee shall be filled according to this
Section 1.

        2.     Agreement to Vote for Mayfield Nominee.

               a. During the term of this Voting Agreement, each of the
Investors agrees to vote all of its Series A Shares, Series B Shares, Series C
Shares, Series D Shares and Series E Shares now or hereafter owned by it to
elect one (1) nominee of Mayfield (the "Mayfield Nominee") as a Preferred
Director.

               b. Prior to each election of directors of the Company, Mayfield
shall designate the Mayfield Nominee in writing to the Company. The Company
shall promptly notify each of the Investors of Mayfield's choice of such
nominee. Any vacancy occurring because of the death, resignation, removal or
disqualification of the Mayfield Nominee shall be filled according to this
Section 2.

        3.     Agreement to Vote for Crosspoint Nominee.

               a. During the term of this Voting Agreement, each of the
Investors agrees to vote all of its Series A Shares, Series B Shares, Series C
Shares, Series D Shares and Series E Shares now or hereafter owned by it to
elect one (1) nominee of Crosspoint (the "Crosspoint Nominee") as a Preferred
Director.

               b. Prior to each election of directors of the Company, Crosspoint
shall designate the Crosspoint Nominee in writing to the Company. The Company
shall promptly notify each of the Investors of Crosspoint's choice of such
nominee. Any vacancy occurring because of the death, resignation, removal or
disqualification of the Crosspoint Nominee shall be filled according to this
Section 3.

        4.     Agreement to Vote for Axys Nominee.

               a. During the term of this Voting Agreement, each of the
Investors agrees to vote all of its Series A Shares, Series B Shares, Series C
Shares, Series D Shares and Series E Shares now or hereafter owned by it to
elect one (1) nominee of Axys (the "Axys Nominee") as a Preferred Director.

               b. Prior to each election of directors of the Company, Axys shall
designate the Axys Nominee in writing to the Company. The Company shall promptly
notify each of the Investors of Axys' choice of such nominee. Any vacancy
occurring because of the death, resignation, removal or disqualification of the
Axys Nominee shall be filled according to this Section 3.

                                       2
<PAGE>   3
        5. Covenants of the Investors and the Company. The Company, Axys and the
Investors agree to use their reasonable best efforts to ensure that the rights
given to Axys and the Investors hereunder are effective and that Axys and the
Investors shall enjoy the benefits hereof. Such reasonable best efforts shall
include, without limitation, the use of the Company's, Axys' and the Investors'
reasonable best efforts to cause the nomination of the Enterprise Nominee, the
Mayfield Nominee, the Crosspoint Nominee and the Axys Nominee at each election
of the Board of Directors. Neither the Company, Axys nor any of the Investors
shall, by any voluntary action, avoid or seek to avoid the observance or
performance of any of the terms to be performed hereunder by the Company, Axys
or the Investors, respectively, but shall at all times in good faith assist in
the carrying out of all of the provisions of this Voting Agreement and shall use
their reasonable best efforts to protect the rights of the Investors and Axys
hereunder against impairment.

        6.     Successors and Assigns.

               a. The Investors' rights under this Agreement are not assignable
without the prior written consent of the Company and the holders of a majority
of the Preferred Stock then held by the Investors (the "Majority Investors"),
which consent may be withheld for any reason whatsoever. Axys' rights under this
Agreement are not assignable without the prior written consent of the Company,
which consent may be withheld for any reason whatsoever. Notwithstanding the
foregoing, Axys shall be allowed to make a bona fide pledge of its Company
Common Stock and Axys' rights under this Agreement may be assigned, on an
indivisible basis, to any person if both the following conditions apply: (i) the
assignment to such person is part of the enforcement against Axys' shares of
Company Common Stock of a security interest which Axys had, via a bona fide
pledge, granted to a lender, and (ii) the assignee complies with Section 6(b)
below.

               b. The burdens of this Voting Agreement shall be binding upon the
successors and assigns to whom the Investors transfer any of their respective
Series A Shares, Series B Shares, Series C Shares, Series D Shares and/or Series
E Shares. The Company shall not permit the transfer of any Series A Shares,
Series B Shares, Series C Shares, Series D Shares and/or Series E Shares on its
books or issue a new certificate representing any Series A Shares, Series B
Shares, Series C Shares, Series D Shares and/or Series E Shares unless and until
the person to whom such security is to be transferred shall have executed a
written agreement, reasonably satisfactory in form and substance to the Majority
Investors and the Company, pursuant to which such person becomes a party to this
Voting Agreement and agrees to be bound by all the burdens hereof as if such
person was an Investor hereunder.

               c. The provisions hereof shall inure to the benefit of, and be
binding upon, the successors and assigns of the Company. Without limitation on
any other rights of assignment, the parties acknowledge that if the Company
reincorporates in Delaware this Agreement shall be assigned to the new Delaware
corporation and the rights and obligations of the parties shall persist as if
all references herein to "the Company" were references to such Delaware
corporation.

                                       3
<PAGE>   4
        7. Legends. Each certificate representing any Series A Shares, Series B
Shares, Series C Shares, Series D Shares or Series E Shares held by the
Investors shall be endorsed by the Company with the following legend:

                THE SHARES EVIDENCED HEREBY ARE SUBJECT TO A VOTING AGREEMENT (A
                COPY OF WHICH MAY BE OBTAINED FROM THE ISSUER), AND BY ACCEPTING
                ANY INTEREST IN SUCH SHARES THE PERSON ACCEPTING SUCH INTEREST
                SHALL BE DEEMED TO AGREE TO AND SHALL BECOME BOUND BY ALL THE
                BURDENS OF SAID VOTING AGREEMENT.

        8. Termination. This Voting Agreement shall terminate upon the earlier
of (i) the consummation of the Company's initial public offering on a firm
underwriting basis, (ii) the closing of a consolidation or merger of the Company
with or into any other corporation or corporations, or a sale, conveyance or
disposition of all or substantially all of the assets of the Company or the
effectuation by the Company of a transaction or series of related transactions
in which more than 50% of the voting power of the Company is disposed of, (iii)
as to each Investor, that date when such Investor (a) holds less than 750,000
Series B Shares and/or Series A Shares, (b) holds less than 100,000 Series C
Shares or Series D Shares, and (c) holds less than 100,000 Series E Shares, or
(iv) as to Axys, that date when Axys holds less than 750,000 shares of the
Company's Common Stock.

        9. Amendments and Waivers. Any term hereof may be amended and the
observance of any term hereof may be waived (either generally or in a particular
instance and either retroactively or prospectively) only with the written
consent of the Company, the Majority Investors or their successors and permitted
assigns and Axys or its successors or permitted assigns. Any amendment or waiver
so effected shall be binding upon the Company, Axys and all of the Investors,
their successors and assigns.

        10. Severability. Whenever possible, each provision of this Voting
Agreement shall be interpreted in such manner as to be effective and valid under
applicable law, but if any provision of this Voting Agreement shall be held to
be prohibited by or invalid under applicable law, such provision shall be
ineffective only to the extent of such prohibition or invalidity, without
invalidating the remainder of such provision or the remaining provisions of this
Voting Agreement.

        11. Governing Law. This Agreement shall be governed by and construed
under the laws of the State of California, without regard to the conflict of
laws provisions thereof.

        12. Notices. All notices, requests and other communications to the
Company or any of the Investors hereunder shall be in writing (including
telecopy or similar electronic transmissions), shall refer specifically to this
Voting Agreement and shall be personally delivered or sent by telecopy or other
electronic facsimile transmission, overnight delivery with a nationally
recognized overnight delivery service or by registered or certified mail, return
receipt

                                       4
<PAGE>   5
requested, postage prepaid, in each case to the respective address specified
below (or such other address as may be specified in writing to the other parties
hereto):

                      a.     If to the Company, to:

                                    DISCOVERY PARTNERS INTERNATIONAL, INC.
                                    9640 Towne Center Drive
                                    San Diego, CA  92121
                                    Attention: Chief Executive Officer
                                    Fax No.:   (858) 455-8088

                      b.     If to Enterprise, to:

                                    ENTERPRISE PARTNERS
                                    7979 Ivanhoe Avenue, Suite 550
                                    La Jolla, California 92037
                                    Attention: Andrew E. Senyei,
                                               General Partner
                                    Fax No.:   (858) 454-2489

                      c.     If to Mayfield, to:

                                    MAYFIELD ASSOCIATES
                                    2800 Sand Hill Road
                                    Menlo Park, CA  94025
                                    Attention: A. Grant Heidrich,
                                               General Partner
                                    Fax No.:   (650) 854-5712

                      d.     If to Crosspoint, to:

                                    CROSSPOINT VENTURE PARTNERS
                                    18552 MacArthur Boulevard, Suite 400
                                    Irvine, CA  92715
                                    Attention: General Partner
                                    Fax No.:   (714) 852-9804

                      e.     If to Agilent, to:

                                    AGILENT TECHNOLOGIES, INC.
                                    3000 Hanover Street
                                    Palo Alto, CA  94304
                                    Attention: Director, Corporate Development
                                    Fax No.:   (650) 852-8432

                             With a copy to:

                                    AGILENT TECHNOLOGIES, INC.

                                       5
<PAGE>   6
                                    3000 Hanover Street
                                    Palo Alto, CA  94304
                                    Attention: General Counsel
                                    Fax No.:   (650) 852-8019

                      f.     If to Pacific, to:

                                    PACIFIC VENTURE GROUP
                                    15635 Alton Parkway, Suite 230
                                    Irvine, CA  92618
                                    Attention: Ralph C. Sabin
                                    Fax No.:   (949) 753-8932

                      g.     If to BayStar, to:

                                    BAYSTAR CAPITAL
                                    425 Market Street, 22nd Floor
                                    San Francisco, CA  94105
                                    Attention: Sherrill Lybrook, Principal
                                    Fax No.:   (415) 512-6472

                      h.     If to Trubitt, to:

                                    HAYDEN J. TRUBITT
                                    Brobeck, Phleger & Harrison LLP
                                    12390 El Camino Real
                                    San Diego, CA  92130
                                    Fax No.:   (858) 720-2555

                      i.     If to Axys, to:

                                    AXYS PHARMACEUTICALS, INC.
                                    180 Kimball Way
                                    South San Francisco, CA 94080
                                    Fax No.:   (650) 829-1067
                                    Attention: William J. Newell, Esq.

                             with a copy to:

                                    COOLEY GODWARD, LLP
                                    Five Palo Alto Square
                                    3000 El Camino Real
                                    Palo Alto, CA 94306-2155
                                    Fax No.:   (650) 849-7400
                                    Attention: Alan C. Mendelson, Esq.

                                       6
<PAGE>   7
Any notice or communication given in conformity with this Section 12 shall be
deemed to be effective when received by the addressee, if delivered by hand,
telecopy or electronic transmission, one (1) day after deposit with a nationally
recognized overnight delivery service and three (3) days after mailing, if
mailed.

        13. Equitable Remedies. The Company, the Investors and Axys acknowledge
and agree that the legal remedies available to the Investors and/or Axys in the
event any party violates the covenants and agreements made in this Voting
Agreement would be inadequate and that the Investors and/or Axys shall be
entitled, without posting any bond or other security, to temporary, preliminary,
and permanent injunctive relief, specific performance and other equitable
remedies in the event of such a violation, in addition to any other remedies
which the Investors and/or Axys may have at law or in equity.

        14. Counterparts. This Voting Agreement may be executed in any number
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 hereto have executed this Amendment No.
3 to Voting Agreement as of the date first written above.

DISCOVERY PARTNERS, INC., a California corporation

By:  /s/ Riccardo Pigliucci
     -------------------------------------------
     Riccardo Pigliucci, Chief Executive Officer

ENTERPRISE PARTNERS III, L.P.

By:  Enterprise Management Partners III, L.P., Its General Partner

By:  /s/ Andrew Senyei
     -------------------------------------------
     General Partner

                                       7
<PAGE>   8
ENTERPRISE PARTNERS III ASSOCIATES, L.P.

By:  Enterprise Management Partners III, L.P., Its General Partner

By:  /s/ Andrew Senyei
     -------------------------------------------
     General Partner

MAYFIELD VIII, a California Limited Partnership

By:  MAYFIELD VIII MANAGEMENT, L.L.C., a Delaware Limited Liability
     Company, its General Partner

By:      /s/ A. Grant Heidrich, III
         --------------------------------------
Title:
         --------------------------------------

MAYFIELD ASSOCIATES FUND II, a California Limited Partnership

By:      /s/   A. Grant Heidrich, III
         --------------------------------------
         General Partner

CROSSPOINT VENTURE PARTNERS-1996

By:      /s/ Donald B. Milder
         --------------------------------------
         General Partner

CROSSPOINT VENTURE PARTNERS LS-1997

By:      /s/ Donald B. Milder
         --------------------------------------
         General Partner

                                       8
<PAGE>   9

AXYS PHARMACEUTICALS, INC., a Delaware corporation

By:    /s/ William J. Newell
       --------------------------------------
       William J. Newell, Senior Vice President

                                       9
<PAGE>   10
                     DISCOVERY PARTNERS INTERNATIONAL, INC.
                       AMENDMENT NO. 4 TO VOTING AGREEMENT

        This Amendment No. 4 to Voting Agreement (the "Amendment") is made as of
June 30, 2000 by and among Discovery Partners International, Inc., a California
corporation formerly known as IRORI (the "Company"), Enterprise Partners III,
L.P., Enterprise Partners III Associates, L.P. (together, "Enterprise"),
Mayfield VIII, Mayfield Associates Fund II (together, "Mayfield"), Crosspoint
Venture Partners-1996, Crosspoint Venture Partners LS-1997 (together,
"Crosspoint"), Agilent Technologies, Inc. (formerly Hewlett-Packard Company)
("Agilent"), Pacific Venture Group II, L.P. ("Pacific"), BayStar Capital, L.P.
and BayStar International Ltd. (together "BayStar"), Hayden J. Trubitt
("Trubitt"), Axys Pharmaceuticals, Inc. ("Axys") and PVG Associates II, L.P.
("PVG Associates), with reference to the Voting Agreement dated as of November
5, 1996 (together with Amendment No. 1 dated October 31, 1997, Amendment No. 2
dated April 7, 2000 and Amendment No. 3 dated April 28, 2000, the "Voting
Agreement"), among the Company, Enterprise, Mayfield, Crosspoint, Agilent,
Pacific, Baystar, Trubitt and Axys. Enterprise, Mayfield, Crosspoint, Agilent,
Pacific, Baystar, Trubitt and Axys are collectively referred to herein as the
"Existing Investors." Capitalized terms not otherwise defined herein shall have
the meanings set forth in the Voting Agreement.

                                    RECITALS

        A. Pacific desires to transfer 11,044 Series E Shares to PVG Associates;

        B. The Company and the Existing Investors desire that PVG Associates,
through this Amendment, enters into and becomes a part of this Voting Agreement,
having all rights and obligations of an Investor thereunder.

                                    AGREEMENT

        NOW, THEREFORE, in consideration of the mutual covenants set forth
herein, and for other good and valuable consideration the receipt of which is
hereby acknowledged, the parties agree as follows:

        1. Additional Party to the Voting Agreement. Pursuant to Section 9 of
the Voting Agreement, the Voting Agreement is hereby amended to include PVG
Associates as an Investor and PVG Associates shall be considered to be an
Investor for all purposes under the Voting Agreement.

        2. Amendments to Voting Agreement.

               (a) BayStar is confirmed to be an Investor at and after the date
of the Voting Agreement.

               (b) The parties confirm that the Voting Agreement has terminated
as to Trubitt due to Section 8(iii) of the Voting Agreement.

<PAGE>   11

               (c) For the purpose of the 100,000 Series E Shares threshold of
Section 8(iii)(c) of the Voting Agreement, all Series E Shares held by Pacific
and PVG Associates shall be deemed to be held by Pacific and shall also be
deemed to be held by PVG Associates.

        3. Effect of Amendment. Except as expressly modified by this Amendment,
the Voting Agreement shall remain unmodified and in full force and effect.

        4. 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.

        5. Severability. In the event one or more of the provisions of this
Amendment should, for any reason, be held to be invalid, illegal or
unenforceable in any respect, such invalidity, illegality or unenforceability
shall not affect any other provisions of this Amendment, and this Amendment
shall be construed and interpreted in such manner as to be effective and valid
under applicable law.

                [REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK]

                                       2
<PAGE>   12
        IN WITNESS WHEREOF, the parties hereto have executed this Amendment as
of the day and year first above written.

                                Discovery Partners International, Inc., a
                                California corporation (formerly known as IRORI)

                                By: /s/ Riccardo Pigliucci
                                    --------------------------------------------
                                    Riccardo Pigliucci, Chief Executive Officer

                                INVESTORS:

                                ENTERPRISE PARTNERS III, L.P.

                                By:     Enterprise Management Partners III,
                                        L.P., Its General Partner

                                        By: /s/ Andrew Senyei
                                            ------------------------------------
                                            General Partner, Andrew E. Senyei,
                                              M.D.

                                ENTERPRISE PARTNERS III ASSOCIATES, L.P.

                                By:     Enterprise Management Partners III,
                                        L.P., Its General Partner

                                        By: /s/ Andrew Senyei
                                            ------------------------------------
                                            General Partner, Andrew E. Senyei,
                                              M.D.

                                PACIFIC VENTURE GROUP II, L.P.

                                By: /s/ Ralph C. Sabin
                                   ---------------------------------------------
                                Its: Managing Director
                                    --------------------------------------------

             [SIGNATURE PAGE TO AMENDMENT NO. 4 TO VOTING AGREEMENT]
<PAGE>   13

                                MAYFIELD VIII, a California Limited Partnership

                                By:      Mayfield VIII Management, L.L.C. a
                                         Delaware limited liability company, its
                                          General Partner

                                         By: /s/ A. Grant Heidrich
                                             -----------------------------------
                                             General Partner

                                MAYFIELD ASSOCIATES FUND II, a California
                                Limited Partnership

                                By:      /s/ A. Grant Heidrich
                                         ---------------------------------------
                                          General Partner

                                CROSSPOINT VENTURE PARTNERS-1996

                                By: /s/ Don Milder
                                    --------------------------------------------
                                       Don Milder, General Partner

                                CROSSPOINT VENTURE PARTNERS LS-1997

                                By: /s/ Don Milder
                                    --------------------------------------------
                                       Don Milder, General Partner

                                AGILENT TECHNOLOGIES, INC., f/k/a
                                Hewlett-Packard Company

                                By:
                                    --------------------------------------------

                                Its:
                                    --------------------------------------------

                                BRISTOL-MYERS SQUIBB COMPANY

                                By:
                                    --------------------------------------------

                                Its:
                                    --------------------------------------------

             [SIGNATURE PAGE TO AMENDMENT NO. 4 TO VOTING AGREEMENT]
<PAGE>   14

                              RHONE-POULENC RORER INTERNATIONAL HOLDINGS, INC.

                              By:
                                    --------------------------------------------

                              Its:
                                    --------------------------------------------

                              BAYSTAR CAPITAL, LLP, a Delaware Limited
                              Partnership

                              By:    BayStar Capital Management, LLC,
                                     Its General Partner

                              By: /s/ Steve Lamar
                                  ----------------------------------------------
                                      Steve Lamar, Vice President

                              BAYSTAR INTERNATIONAL LTD, a British Virgin
                              Islands Corporation

                              By:    BayStar International Management, LLC,
                                     Its General Partner

                              By: /s/ Steve Lamar
                                  ----------------------------------------------
                                      Steve Lamar, Vice President

                              --------------------------------------------------
                                              Hayden J. Trubitt

                              AXYS PHARMACEUTICALS, INC. a Delaware Corporation

                              By: /s/ William J. Newell
                                  ----------------------------------------------
                                      William J. Newell, Senior Vice President

             [SIGNATURE PAGE TO AMENDMENT NO. 4 TO VOTING AGREEMENT]
<PAGE>   15

                              PVG ASSOCIATES II, L.P.

                              By:     PVG Equity Partners II, L.L.C.
                                      its General Partner

                                      By: /s/ Ralph C. Sabin
                                         ---------------------------------------
                                         Ralph C. Sabin, Managing Director

                                      16830 Ventura Boulevard
                                      Suite 244
                                      Encino, California 91436

             [SIGNATURE PAGE TO AMENDMENT NO. 4 TO VOTING AGREEMENT]<PAGE>   1

                                                                    EXHIBIT 10.8

                           INDEMNITY ESCROW AGREEMENT

        This INDEMNITY ESCROW AGREEMENT (this "Agreement"), dated as of April
28, 2000, is by and among Discovery Partners International, Inc., a California
corporation ("DPII"), Axys Pharmaceuticals, Inc., a Delaware corporation
("Axys"), and the institution named on the signature page under "Escrow Agent,"
as Escrow Agent ("Escrow Agent"). Unless otherwise defined herein, all
capitalized terms used in this Agreement shall have the meaning ascribed to such
terms in the Agreement and Plan of Merger dated as of April 11, 2000 (the
"Merger Agreement"), by and among DPII, DPII Newco, LLC, a Delaware limited
liability company and a wholly-owned subsidiary of DPII, Axys Advanced
Technologies, Inc., a Delaware corporation ("AAT") and Axys.

        Accordingly, the parties hereto agree as follows:

        1. Appointment and Acceptance. Axys and DPII hereby appoint Escrow Agent
as escrow agent for the purposes and upon the terms and conditions hereinafter
set forth. Escrow Agent hereby accepts such appointment and agrees to act as
escrow agent hereunder and to hold, invest and dispose of any funds received by
it hereunder in accordance with the terms and conditions hereinafter set forth.

        2. Deposit of Escrowed Consideration. On the date hereof, DPII delivered
to Escrow Agent for deposit in escrow pursuant to the provisions hereof a share
certificate (the "Share Certificate") for 371,250 shares of DPII Common Stock,
made out in favor of Axys (the "Escrowed Consideration").

        3. Purpose of Agreement. DPII and Axys represent that this Agreement has
been executed and the deposit of the Escrowed Consideration hereunder has been
made pursuant to the Merger Agreement for the purpose of providing a fund for
the payment of the first amounts owed (if any) to DPII in connection with the
Merger Agreement ("Covered Claims").

        4. Delivery of Escrowed Consideration.

                (a) Because of the lump nature of the share certificate which
constitutes the initial Escrowed Consideration, the parties agree that in any
case where Escrowed Consideration is to be delivered to DPII hereunder, such
delivery shall be accomplished by delivery of the Share Certificate to DPII;
DPII shall promptly calculate, based on the "Fair Market Value" per share (as
defined below), the number of shares to be cancelled in respect of such
delivery, and shall promptly return to Escrow Agent, for escrow, a new share
certificate (which shall hereafter be considered the "Share Certificate")
representing a number of shares of DPII Common Stock reflecting the reduction
for the number of cancelled shares. Axys hereby authorizes the cancellation of
shares to the extent and in the manner expressly authorized by this Agreement.
For the purposes of this Agreement, the "Fair Market Value" per share of DPII
Common Stock shall be determined as follows:

<PAGE>   2

                        (i) If traded on a securities exchange or through
NASDAQ-NMS, the Fair Market Value shall be deemed to be the average of the
closing price of such share on such exchange over the twenty (20) day period
ending three (3) days prior to the date on which the Escrow Agent is obligated
to deliver any portion of the Escrowed Consideration hereunder; and

                        (ii) If there is no active public market, the Fair
Market Value shall be deemed to be the per share price at which the Company sold
shares of its capital stock in its most recent equity financing negotiated on an
arms'-length basis.

                (b) If at any time prior to the first anniversary of the date
hereof DPII shall claim that it is entitled to payment of all or a portion of
the Escrowed Consideration as a result of any Covered Claim, DPII shall give
notice of such Covered Claim (the "Notice of Covered Claim") to the Escrow
Agent. The Notice of Covered Claim shall describe with reasonable specificity
the event or circumstance giving rise to the Covered Claim and specifying the
amount of the Escrowed Consideration which should be released to satisfy such
Covered Claims. Upon Escrow Agent's receipt of a Notice of Covered Claim from
DPII, Escrow Agent shall promptly deliver a copy thereof to Axys. Within fifteen
(15) business days after delivery by Escrow Agent of a copy of such Notice of
Covered Claim to Axys, Axys may deliver to Escrow Agent a notice (the "Notice of
Dispute") disputing the request for payment of Escrowed Consideration stated in
the Notice of Covered Claim. The Notice of Dispute shall specify the amount
being disputed (the "Disputed Funds"), describing with reasonable specificity
the reasons for such dispute. If Escrow Agent has not received a Notice of
Dispute prior to the expiration of the 15-day period referred to above, then
upon expiration of such 15-day period, the Escrow Agent shall pay to DPII,
within three business days, as provided in Section 4(a) above, the full amount
of the Escrowed Consideration requested in the Notice of Covered Claim. If
Escrow Agent has received a Notice of Dispute which disputes in part the request
for payment of Escrowed Consideration stated in the Notice of Covered Claim,
then Escrow Agent shall pay to DPII, within three business days, as provided in
Section 4(a) above, the amount of Escrowed Consideration requested in the Notice
of Covered Claim which is not Disputed Funds.

                (c) If Escrow Agent receives a Notice of Dispute from Axys,
Escrow Agent shall promptly deliver a copy of the Notice of Dispute to DPII, and
shall not deliver the Disputed Funds (i.e., the Share Certificate in respect of
the Disputed Funds) to DPII until Escrow Agent shall have received one of the
following:

                        i. A certified copy of an order, decree or judgment
issued or rendered by a court of competent jurisdiction, which order, decree or
judgment shall be accompanied by a legal opinion of counsel to DPII that such
judgment has been finally affirmed on appeal or which by lapse of time or
otherwise is no longer subject to appeal (a "Final Decision") with respect to
the Notice of Covered Claim which is the subject of the Notice of Dispute; or

                        ii. A joint written direction executed by DPII and Axys
directing the distribution of the relevant portion of the Escrowed
Consideration.

                                       2
<PAGE>   3

Upon receipt of either (i) or (ii) above, Escrow Agent shall deliver the
relevant portion of the Escrowed Consideration, within three business days, by
delivery of the Share Certificate to DPII in accordance with the terms of such
Final Decision or joint direction, as the case may be.

                (d) On the first anniversary of the date hereof, any Escrowed
Consideration which is not Disputed Funds or the subject of an unresolved Notice
of Covered Claim shall be paid to Axys. To effect this, Escrow Agent shall
deliver the Share Certificate to DPII, and DPII shall issue and deliver to Axys
as provided in Section 6(b) below a share certificate for the shares which are
not Disputed Funds and are not the subject of an unresolved Notice of Covered
Claim; and DPII shall issue and deliver to the Escrow Agent, for escrow, a new
Share Certificate in Axys' name for the remainder, if any, of the shares.

        5. Investment of Escrowed Consideration. Escrow Agent shall invest any
cash dividends on or other cash processed of the Escrowed Consideration, from
time to time, in investments jointly designated in writing by DPII and Axys or,
in the absence of such designation, in a money-market fund. The investments of
Escrowed Consideration may be executed by Escrow Agent's own investment
department. The interest and investment proceeds of all investments made
hereunder shall be retained as part of the escrow as Escrowed Consideration and
distributed as provided herein with respect to the Escrowed Consideration.
Escrow Agent shall deliver monthly statements to DPII and Axys in accordance
with Escrow Agent's regular practice; the parties hereby agree that, except for
the foregoing, Escrow Agent shall have no obligations to monitor, or advise the
parties with respect to, such investments.

        6. Termination of Escrow.

                (a) Except as set forth in Section 6(b), this Agreement shall
terminate upon the earliest of (i) the receipt by Escrow Agent of written notice
of termination executed by both DPII and Axys directing the distribution of all
property then held by Escrow Agent under and pursuant to the Agreement, (ii)
when all Escrowed Consideration (and all interest and investments in which any
of the Escrowed Consideration shall have been invested) shall have been
distributed by Escrow Agent in accordance with the terms of this Agreement; or
(iii) the first anniversary of the Closing Date.

                (b) Notwithstanding Section 6(a), in the event that upon the
first anniversary of the Closing Date, there remains in the escrow, any portion
of the Escrowed Consideration which is Disputed Funds or the subject of an
unresolved Notice of Covered Claim, then this Agreement shall not terminate on
such first anniversary with respect to such funds and shall continue until the
resolution of the dispute pursuant to Section 4(b). Any Escrowed Consideration
which is not Disputed Funds or subject to an unresolved Notice of Covered Claim
shall be delivered to Axys within three business days of the termination of the
Agreement. To effect this, Escrow Agent shall deliver the Share Certificate to
DPII, and DPII shall issue and deliver to Axys a share certificate for the
shares which are not Disputed Funds and are not the subject of an unresolved
Notice of Covered Claim; and DPII shall issue and deliver to the Escrow Agent,
for escrow, a new Share Certificate in Axys' name for the remainder of the
shares.

                                       3
<PAGE>   4

                        (c) Escrow Agent is authorized to liquidate the
securities (other than DPII shares) held hereunder to the extent necessary to
distribute the Escrowed Consideration as provided herein and shall have no
liability for any loss arising out of any such liquidation.

        7. Notices. All notices, requests and other communications hereunder
must be in writing and will be deemed to have been duly given only if delivered
personally or by facsimile transmission with answer back confirmation or mailed
(first class, postage prepaid) or by overnight courier to the parties at the
addresses or facsimile numbers set forth below such party's signature to this
Agreement. All such notices, requests and other communications will (i) if
delivered personally or by overnight courier to the address as provided in this
Section, be deemed given upon delivery, (ii) if delivered by facsimile
transmission to the facsimile number as provided in this Section, be deemed
given upon sending, and (iii) if delivered by mail in the manner described above
to the address as provided in this Section, be deemed given two business days
after mailing (in each case regardless of whether such notice, request or other
communication is received by any other person to whom a copy of such notice,
request or other communication is to be delivered pursuant to this Section). Any
party from time to time may change its address, facsimile number or other
information for the purpose of notices to that party by giving notice specifying
such change to the other parties hereto.

        8. Escrow Agent's Liability. Escrow Agent undertakes to perform such
duties and only such duties as are specifically set forth in this Agreement, and
no implied covenants or obligations shall be read into this Agreement against
Escrow Agent. In the absence of bad faith, gross negligence or willful
misconduct on its part, Escrow Agent may conclusively rely, as to the truth of
the statements and the correctness of the opinions expressed therein, upon
certificates or opinions furnished to Escrow Agent. Escrow Agent may act upon
any instrument, certificate, opinion or other writing believed by it in good
faith and without gross negligence to be genuine, and shall not be liable in
connection with the performance by it of its duties pursuant to the provisions
of the Agreement, except for its own bad faith, gross negligence or willful
misconduct. Escrow Agent may consult with counsel of its own choice and shall
have full and complete authorization and protection for any action taken,
suffered or omitted by it hereunder in good faith and in accordance with the
opinion of such counsel. Escrow Agent may execute powers hereunder or perform
any duties hereunder either directly or by or through agents or attorneys.

        9. Indemnification of Escrow Agent. Axys and DPII shall jointly and
severally indemnify and hold harmless Escrow Agent (and any successor Escrow
Agent) for any loss, liability or expense incurred without gross negligence,
willful misconduct or bad faith on the part of Escrow Agent, arising out of or
in connection with its entering into the Agreement, carrying out its duties
hereunder and accepting the Escrowed Consideration, including the costs and
expenses of defending itself against any claim of liability in connection with
the exercise or performance of any of its powers or duties hereunder (including
reasonable fees, expenses and disbursements of its counsel). Axys and DPII agree
to promptly reimburse the other party for any payments to Escrow Agent under
this Section 9 as necessary in order to ensure that all such payments are shared
equally by Axys and DPII.

        10. Escrow Agent to Follow Instructions of DPII and Axys.
Notwithstanding any provision contained herein to the contrary, Escrow Agent
shall at any time and from time to time

                                       4
<PAGE>   5

take such action hereunder with respect to the Escrowed Consideration (and the
investments in which any of the Escrowed Consideration shall have been invested)
as shall be directed in writing by both DPII and Axys.

        11. Resignation of Escrow Agent. Escrow Agent, or any successor, may
resign at any time upon giving written notice, thirty (30) days before such
resignation shall take effect, to DPII and Axys. In the event Escrow Agent shall
resign or be unable to serve, it shall be succeeded by such bank or trust
company as DPII and Axys shall appoint, or if no appointment is made, by a bank
or trust company appointed by a court of competent jurisdiction. In the absence
of a successor so appointed by DPII and Axys, Escrow Agent may petition such a
court to appoint a successor escrow agent. The resigning escrow agent shall
transfer to its successor all money, securities and investments then held
subject to this escrow and all pending notices, instructions and directions then
in its possession, and shall thereupon be discharged, and the successor shall
thereupon succeed to all the rights, powers and duties and shall assume all of
the obligations of the resigning escrow agent.

        12. Escrow Agent's Fees.

                (a) Escrow Agent shall be entitled to a fee for services
rendered according to the fee schedule attached hereto. One half of such fees
shall be paid by Axys and one-half of such fees shall be paid by DPII.

                (b) In case Escrow Agent becomes involved in litigation on
account of the property deposited hereunder or this Agreement, it shall have the
right to retain counsel. One half of any and all costs, attorneys' fees,
charges, disbursements, and expenses in connection with such litigation shall be
paid by Axys and one-half of such fees shall be paid by DPII.

                (c) Axys and DPII agree to promptly reimburse the other party
for any payments to Escrow Agent under this Section 12 in order to ensure that
all such payments are shared equally by Axys and DPII.

        13. Escrow Agent's Reaction to Disputes.

                (a) In case the Escrowed Consideration shall be attached,
garnished, or levied upon any court order, or the delivery thereof shall be
stayed or enjoined by an order of court, or any order, judgment or decree shall
be made or entered by any court affecting the property deposited under this
Agreement, or any part thereof, Escrow Agent is hereby expressly authorized in
its sole direction, to obey and comply with all writs, orders or decrees so
entered or issued, which it is advised by legal counsel of its own choosing is
binding upon it, whether with or without jurisdiction, and in case Escrow Agent
obeys or complies with any such writ, order or decree it shall not be liable to
any of the parties hereto or to any other person, firm or corporation, by reason
of such compliance notwithstanding such writ, order or decree is subsequently
reversed, modified, annulled, set aside or vacated.

                (b) In case conflicting demands are made upon it for any
situation not addressed in this Agreement, Escrow Agent may withhold performance
of this escrow with respect to matters related to such conflicting demands until
such time as said conflicting

                                       5
<PAGE>   6

demands shall have been withdrawn or the rights of the respective parties shall
have been settled by court adjudication, arbitration, joint order or otherwise.

        14. Assignment. The obligations imposed and the rights conferred by this
Escrow Agreement shall be binding upon and inure to the benefit of the
respective successors and assigns of the parties hereto.

        15. Governing Law, Consent to Jurisdiction and Forum Selection. This
Indemnity Escrow Agreement shall be governed by and construed in accordance with
the laws of the State of California, without giving effect to principles of
conflicts of law. The parties hereto agree that all actions or proceedings
arising in connection with this Agreement (as to proceedings initiated by Axys)
shall be initiated and tried exclusively in the State and Federal courts located
in the County of San Diego, State of California. The parties hereto agree that
all actions or proceedings arising in connection with this Agreement (as to
proceedings initiated by DPII or Escrow Agent) shall be initiated and tried
exclusively in the State and Federal courts located in the County of San
Francisco, State of California. The aforementioned choice of venue is intended
by the parties to be mandatory and not permissive in nature, thereby precluding
the possibility of litigation between the parties with respect to or arising out
of this Agreement in any jurisdiction other than that specified in this Section
15. Each party hereby waives any right it may have to assert the doctrine of
forum non conveniens or similar doctrine or to object to venue with respect to
any proceeding brought in accordance with this paragraph, and stipulates that
the State and Federal courts located in the County of San Diego, State of
California (as to proceedings initiated by Axys) or in the County of San
Francisco, State of California (as to proceedings initiated by DPII or Escrow
Agent) shall have in personam jurisdiction and venue over each of them for the
purposes of litigating any dispute, controversy or proceeding arising out of or
related to this Agreement. Each party hereby authorizes and accepts service of
process sufficient for personal jurisdiction in any action against it as
contemplated by this Section 15 by registered or certified mail, return receipt
requested, postage prepaid, to its address for the giving of notices as set
forth in this Agreement, or in the manner set forth in Section 7 of this
Agreement for the giving of notice. Any final judgment rendered against a party
in any action or proceeding shall be conclusive as to the subject of such final
judgment and may be enforced in other jurisdictions in any manner provided by
law.

        16. Entire Agreement. This Agreement, together with the Merger
Agreement, with respect to which the Escrow Agent is not a party (including the
schedules and exhibits thereto and the other agreements contemplated thereby),
contains the entire agreement between the parties hereto with respect to the
transactions contemplated herein.

        17. Amendment. This Agreement cannot be terminated, altered or amended
except pursuant to an instrument in writing signed by DPII, Axys and Escrow
Agent.

        18. Merger, Conversion, Consolidation or Succession to Business.

                (a) Any corporation into which Escrow Agent may be merged or
converted or with which it may be consolidated, or any corporation resulting
from any merger, conversion or consolidation to which Escrow Agent shall be a
party, or any corporation succeeding to all or substantially all of the
corporate trust business of Escrow Agent, shall be the successor of

                                       6
<PAGE>   7

Escrow Agent hereunder without the execution or filing of any paper or any
further act on the part of any of the parties hereto.

                (b) Any corporation into which DPII or Axys may be merged or
converted or with which it may be consolidated, or any corporation resulting
from any merger, conversion or consolidation to which DPII or Axys shall be a
party, shall be the successor of DPII or Axys hereunder without the execution or
filing of any paper or any further act on the part of any of the parties hereto.

        19. Enforceability. If any provision hereof shall be held invalid or
unenforceable, such invalidity or unenforceability shall attach only to such
provision and shall not in any manner affect or render invalid or unenforceable
any other provision of this Indemnity Escrow Agreement, and the Agreement shall
be carried out as if any such invalid or unenforceable provision were not
contained herein.

        20. Distributions. Distributions of the Escrowed Consideration to DPII
pursuant to this Agreement shall be deemed to be reductions of the merger
consideration paid under the Merger Agreement.

        21. Counterparts. This Agreement may be executed in any number of
counterparts, each of which shall be deemed an original and all of which
together shall constitute one and the same instrument.

        [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]

                                       7
<PAGE>   8

        IN WITNESS WHEREOF, the parties hereto have caused this Indemnity Escrow
Agreement to be signed as of the date first above written.

                                         AXYS PHARMACEUTICALS, INC.,
                                         a Delaware corporation

                                         By: /s/ William T. Newell
                                            ------------------------------------
                                            Name:  William T. Newell
                                            Title: Senior Vice President

                               Address:  180 Kimball Way
                                         South San Francisco, CA 94080
                                         Attn: Chief Executive Officer
                                           Fax: (650) 829-1067

                                         DISCOVERY PARTNERS INTERNATIONAL, INC.,
                                         a California corporation

                                         By: /s/ Riccardo Pigliucci
                                            ------------------------------------
                                            Name:  Ricardo Pigliucci
                                            Title: Chairman and CEO

                               Address:  9640 Towne Centre Drive
                                         San Diego, CA 92121
                                         Attn: Chief Executive Officer
                                           Fax: (858) 455-8088

                          ESCROW AGENT:  U.S. TRUST COMPANY NATIONAL ASSOCIATION

                                         By: /s/ M. Deborah Gibbons
                                            ------------------------------------
                                            Name:  M. Deborah Gibbons
                                            Title: Vice President

                               Address:  515 South Flower, Suite 2700
                                         Los Angeles, CA 90071

                 [SIGNATURE PAGE TO INDEMNITY ESCROW AGREEMENT]

                                       8

Source: [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00012-of-00352.parquet"}, [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00012-of-00352.parquet"}]]