<PAGE>
                                                                   Exhibit 10.20

[*] CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY
    BRACKETS, HAS BEEN OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND
    EXCHANGE COMMISSION PURSUANT TO RULE 406 OF THE SECURITIES EXCHANGE ACT OF
    1933, AS AMENDED.


                                           280 East Grand Avenue
                                           South San Francisco, CA 94080
[CYTOKINETICS LOGO]                        Tel (650) 624-3000 Fax (650) 624-3010

November 5, 2002

Glaxo Group Limited, doing business as GlaxoSmithKline
709 Swedeland Road
King of Prussia, Pennsylvania 19406
Attn: Pradip K. Bhatnagar, Ph.D., Director, Genetic & Discovery Alliances

RE: ASSIGNMENT OF GSK MEDICINAL CHEMISTRY PERSONNEL TO HIT-TO-LEAD ACTIVITIES
UNDER THAT CERTAIN COLLABORATION AND LICENSE AGREEMENT BY AND BETWEEN GLAXO
GROUP LIMITED, A GLAXOSMITHKLINE COMPANY, ("GSK") AND CYTOKINETICS, INC. ("CK")
OF EVEN DATE JUNE 20, 2001 (the "COLLABORATION AGREEMENT")

Dear Pradip:

Pursuant to this letter amendment to the Collaboration Agreement (the "Letter
Amendment"), GSK desires to assign certain medicinal chemistry personnel within
GSK to perform hit-to-lead activities as part of the Research Program under the
Collaboration Agreement, all on the terms set forth herein.

Now therefore, GSK and CK agree, effective as of November 5, 2002 (the "Letter
Amendment Effective Date"), as follows:

         1.       All capitalized terms not defined herein shall have the
                  meaning ascribed to them in the Collaboration Agreement.

         2.       GSK may assign medicinal chemistry personnel (other than CK
                  FTEs) within GSK's high-throughput chemistry resource (the
                  "HTC Resource") at the rate (i.e., a running rate) of [*]
                  ([*]) full-time equivalents or more, solely to perform
                  Hit-To-Lead activities under the Research Program relating to
                  a particular Mitotic Kinesin Target, without such assignment
                  and Hit-To-Lead activities accruing toward the [*] ([*]) FTE
                  limit of establishing a [*] Program pursuant to Section
                  2.6.2(a).

         3.       Notwithstanding the foregoing, if a Tractable Compound has
                  been identified with respect to a particular Mitotic Kinesin
                  Target, the assignment by GSK of any medicinal chemistry
                  personnel (other than CK FTEs) to perform activities relating
                  to such Mitotic Kinesin Target, including without limitation
                  any medicinal chemistry personnel within the HTC Resource and
                  regardless of the activities of such personnel, shall accrue
                  towards the [*] ([*]) FTE limit of establishing a [*] Program
                  pursuant to Section 2.6.2(a).


* Certain information on this page has been omitted and filed separately with
  the Commission. Confidential treatment has been requested with respect to the
  omitted portions.

<PAGE>

Pradip K. Bhatnagar, Ph.D.
November 5, 2002
Page Two

         4.       As used herein, "Hit-To-Lead" shall mean those activities
                  directed to the process of synthesizing and identifying active
                  new chemical entities up to and including identification of a
                  compound that meets the Tractable Compound Criteria. It is
                  understood that activities directed to the subsequent
                  synthetic modification and testing of a Tractable Compound are
                  not included in Hit-To-Lead.

         5.       Except as specifically modified or amended hereby, the
                  Collaboration Agreement shall remain in full force and effect
                  and, as modified or amended, is hereby ratified, confirmed and
                  approved. No provision of this Letter Amendment may be
                  modified or amended except expressly in a writing signed by
                  both parties nor shall any terms be waived except expressly in
                  a writing signed by the party charged therewith. This Letter
                  Amendment shall be governed in accordance with the laws of the
                  [*], without regard to principles of conflicts of laws.

Please sign and return two copies of this letter if you agree to the foregoing
terms.

Sincerely,

/s/ Robert I. Blum
-------------------------
Robert I. Blum
Senior Vice President, Finance and Corporate Development
Chief Financial Officer
Cytokinetics, Inc.

Agreed and accepted:

GLAXO GROUP LIMITED

/s/ Pradip K Bhatnagar
--------------------------

Name: PRADIP K BHATNAGAR

Title: DIRECTOR, Genetic & Discovery Alliances

cc: Vice President, Business Development, Glaxo Group Limited, doing
    business as GlaxoSmithKline
    Senior Vice President and Assistant General Counsel-R&D Legal Operations,
    GlaxoSmithKline Corporate Legal Department
    Kenneth A. Clark, Esq., Wilson Sonsini Goodrich & Rosati Professional
    Corporation

* Certain information on this page has been omitted and filed separately with
  the Commission. Confidential treatment has been requested with respect to the
  omitted portions.