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                                                                  Exhibit 10.4

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER
THE SECURITIES ACT OF 1933, AS AMENDED, AND MAY NOT BE SOLD, PLEDGED OR
OTHERWISE TRANSFERRED WITHOUT AN EFFECTIVE REGISTRATION THEREOF UNDER SUCH ACT
OR PURSUANT TO RULE 144 OR AN OPINION OF COUNSEL REASONABLY SATISFACTORY TO THE
CORPORATION AND ITS COUNSEL THAT SUCH REGISTRATION IS NOT REQUIRED.

                            WARRANT TO PURCHASE STOCK

<Table>
          <S>                      <C>
          Corporation:             COMBINATORX, INCORPORATED, a Delaware corporation
          Number of Shares:        128,000 (subject to adjustment pursuant to Article 2)
          Class of Stock:          $0.001 par value Common Stock
          Initial Exercise Price:  $3.75 per share (subject to adjustment pursuant to Article 2)
          Issue Date:              September 10, 2002
          Expiration Date:         September 9, 2007
</Table>

     THIS WARRANT CERTIFIES THAT, for good and valuable consideration, the
receipt of which is hereby acknowledged, ROCKPORT VENTURE SECURITIES, LLC, a
Delaware limited liability company or its assignee ("Holder") is entitled to
purchase the number of fully paid and nonassessable shares of the class of
securities (the "Shares") of the corporation (the "Company") at the initial
exercise price per Share (the "Warrant Price") all as set forth above and as
adjusted pursuant to Article 2 of this warrant, subject to the provisions and
upon the terms and conditions set forth in this warrant.

ARTICLE 1.   EXERCISE.

     1.1     METHOD OF EXERCISE. Holder may exercise this warrant by delivering
this warrant and a duly executed Notice of Exercise in substantially the form
attached as Appendix 1 to the principal office of the Company. Unless Holder is
exercising the conversion right set forth in Section 1.2, Holder shall also
deliver to the Company a check (for immediately available funds) for the
aggregate Warrant Price for the Shares being purchased.

     1.2     CASHLESS CONVERSION RIGHT. In lieu of exercising this warrant for
cash as specified in Section 1.1, Holder may from time to time convert this
warrant, in whole or in part, into a number of Shares determined by dividing (a)
the aggregate fair market value of the Shares or other securities otherwise
issuable upon exercise of this warrant minus the aggregate Warrant Price of such
Shares by (b) the fair market value of one Share. The fair market value of the
Shares shall be determined pursuant to Section 1.3.

     1.3     FAIR MARKET VALUE. If the Shares are traded regularly in a public
market, the fair market value of the Shares shall be the closing price of the
Shares (or the closing price of the Company's stock into which the Shares are
convertible) reported for the business day immediately before Holder delivers
its Notice of Exercise to the Company. If the Shares are not regularly traded in
a public market, the Board of Directors of the Company shall determine fair
market value in its reasonable good faith judgment.

     1.4     DELIVERY OF CERTIFICATE AND NEW WARRANT. Promptly after Holder
exercises or converts this warrant, the Company shall deliver to Holder
certificates for the Shares acquired and, if this warrant has not been fully
exercised or converted and has not expired, a new warrant representing the
Shares not so acquired.

     1.5     REPLACEMENT OF WARRANTS. On receipt of evidence reasonably
satisfactory to the Company of the loss, theft, destruction or mutilation of
this warrant and, in the case of loss, theft or destruction, on delivery of an
indemnity agreement reasonably satisfactory in form and amount to the Company
or, in the case of mutilation, on surrender and cancellation of this warrant,
the Company at its expense shall execute and deliver, in lieu of this warrant, a
new warrant of like tenor.

     1.6     SALE, MERGER, OR CONSOLIDATION OF THE COMPANY.

             1.6.1  "ACQUISITION." For the purpose of this warrant,
"Acquisition" means any sale, license, or other disposition of all or
substantially all of the assets (including intellectual property) of the
Company, or any

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reorganization, consolidation, or merger of the Company where the holders of the
Company's securities before the transaction beneficially own less than 50% of
the outstanding voting securities of the surviving entity after the transaction.

             1.6.2  AUTOMATIC EXERCISE OF WARRANT. Upon the closing of any
Acquisition, to the extent this warrant has not already been exercised, this
warrant shall be deemed to have been automatically (without the need for any
action on the part of the Holder) exercised immediately prior to the closing of
the said Acquisition by the cashless conversion method described in Section 1.2.

ARTICLE 2.   ADJUSTMENTS TO THE SHARES AND WARRANT PRICE.

     2.1     STOCK DIVIDENDS, SPLITS, ETC. If, after the Issue Date, the
Company declares or pays a dividend on its common stock payable in common stock
or other securities, or subdivides the outstanding common stock into a greater
amount of common stock, then upon exercise of this warrant (to the extent not
already exercised), for each Share acquired, Holder shall receive, without cost
to Holder, the total number and kind of securities to which Holder would have
been entitled had Holder owned the Shares of record as of the date the dividend
or subdivision occurred.

     2.2     RECLASSIFICATION, EXCHANGE OR SUBSTITUTION. Upon any
reclassification, exchange, substitution, or other event that results in a
change of the number and/or class of the securities issuable upon exercise or
conversion of this warrant, Holder shall be entitled to receive, upon exercise
or conversion of this warrant, the number and kind of securities and property
that Holder would have received for the Shares if this warrant had been
exercised immediately before such reclassification, exchange, substitution, or
other event. Such an event shall include any automatic conversion of the
outstanding or issuable securities of the Company of the same class or series as
the Shares to common stock pursuant to the terms of the Company's Certificate of
Incorporation upon the closing of a registered public offering of the Company's
common stock. The Company or its successor shall promptly issue to Holder a new
warrant for such new securities or other property. The new warrant shall provide
for adjustments which shall be as nearly equivalent as may be practicable to the
adjustments provided for in this Article 2 including, without limitation,
adjustments to the Warrant Price and to the number of securities or property
issuable upon exercise of the new warrant. The provisions of this Section 2.2
shall similarly apply to successive reclassifications, exchanges, substitutions,
or other events.

     2.3     ADJUSTMENTS FOR COMBINATIONS, ETC. If the outstanding Shares are
combined or consolidated, by reclassification or otherwise, into a lesser number
of shares, the Warrant Price shall be proportionately increased and the number
of Shares for which this warrant may still be exercised shall be proportionately
decreased. If the outstanding Shares are combined or consolidated, by
reclassification or otherwise, into a greater number of shares, the Warrant
Price shall be proportionately decreased and the number of Shares for which this
warrant may still be exercised shall be proportionately increased.

     2.4     ANTI-DILUTION ADJUSTMENTS. The Warrant Price shall also be subject
to adjustment under the circumstances and in the manner set forth in EXHIBIT A.
Notwithstanding any other provision of this warrant, this warrant may be
exercised for that number of Shares equal to (a) the "Number of Shares"
specified at the top of the first page of this warrant, multiplied by (b) the
"Initial Exercise Price" specified at the top of the first page of this warrant,
divided by (c) the then current Warrant Price as such may have been adjusted
pursuant to the provisions set forth in EXHIBIT A.

     2.5     NO IMPAIRMENT. The Company shall not, by amendment of its
Certificate of Incorporation or through a reorganization, transfer of assets,
consolidation, merger, dissolution, issue, or sale of securities or any other
voluntary action, avoid or seek to avoid the observance or performance of any of
the terms to be observed or performed under this warrant by the Company, but
shall at all times in good faith assist in carrying out all the provisions of
this Article 2 and in taking all such action as may be necessary or appropriate
to protect Holder's rights under this Article against impairment.

     2.6     CERTIFICATE AS TO ADJUSTMENTS. Upon each adjustment of the Warrant
Price, the Company at its expense shall promptly compute such adjustment, and
furnish Holder with a certificate of its Chief Financial Officer setting forth
such adjustment and the facts upon which such adjustment is based. The Company
shall, upon written request, furnish Holder a certificate setting forth the
Warrant Price in effect upon the date thereof and the series of

                                        2
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adjustments leading to such Warrant Price.

ARTICLE 3.   REPRESENTATIONS AND COVENANTS OF THE COMPANY.

     3.1     REPRESENTATIONS AND WARRANTIES. The Company hereby represents and
warrants to the Holder as follows:

             (a)    All Shares which may be issued upon the exercise of the
purchase right represented by this warrant, and all securities, if any, issuable
upon conversion of the Shares, shall, upon issuance, be duly authorized, validly
issued, fully paid and nonassessable, and free of any liens and encumbrances
except for restrictions on transfer provided for herein or under applicable
federal and state securities laws.

             (b)    The Company's capitalization table attached to this warrant
is true and complete as of the Issue Date.

     3.2     NOTICE OF CERTAIN EVENTS. If the Company proposes at any time (a)
to declare any dividend or distribution upon its common stock, whether in cash,
property, stock, or other securities and whether or not a regular cash dividend;
(b) to offer for subscription pro rata to the holders of any class or series of
its stock any additional shares of stock of any class or series or other rights;
(c) to effect any reclassification or recapitalization of common stock; or (d)
to merge or consolidate with or into any other corporation, or sell, lease,
license, or convey all or substantially all of its assets, or to liquidate,
dissolve or wind up, then, in connection with each such event, the Company shall
give Holder (1) at least 20 days prior written notice of the date on which a
record will be taken for such dividend, distribution, or subscription rights
(and specifying the date on which the holders of common stock will be entitled
thereto) or for determining rights to vote, if any, in respect of the matters
referred to in (a) and (b) above; and (2) in the case of the matters referred to
in (c) and (d) above at least 20 days prior written notice of the date when the
same will take place (and specifying the date on which the holders of common
stock will be entitled to exchange their common stock for securities or other
property deliverable upon the occurrence of such event).

     3.3     INFORMATION RIGHTS. So long as the Holder holds this warrant and/or
any of the Shares, the Company shall deliver to the Holder (at the same time as
delivered to the Company's stockholders) the annual audited financial statements
of the Company certified by INDEPENDENT public accountants of recognized
standing.

ARTICLE 4.   MISCELLANEOUS.

     4.1     TERM: NOTICE OF EXPIRATION. This warrant is exercisable in whole or
in part, at any time and from time to time on or before the Expiration Date set
forth above.

     4.2     LEGENDS. This warrant and the Shares (and the securities issuable,
directly or indirectly, upon conversion of the Shares, if any) shall be
imprinted with a legend in substantially the following form:

THIS SECURITY HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS
AMENDED, AND MAY NOT BE SOLD, PLEDGED OR OTHERWISE TRANSFERRED WITHOUT AN
EFFECTIVE REGISTRATION THEREOF UNDER SUCH ACT OR PURSUANT TO RULE 144 OR AN
OPINION OF COUNSEL REASONABLY SATISFACTORY TO THE CORPORATION AND ITS COUNSEL
THAT SUCH REGISTRATION IS NOT REQUIRED.

     4.3     COMPLIANCE WITH SECURITIES LAWS ON TRANSFER. This warrant and the
Shares issuable upon exercise of this warrant (and the securities issuable,
directly or indirectly, upon conversion of the Shares, if any) may not be
transferred or assigned in whole or in part without compliance with applicable
federal and state securities laws by the transferor and the transferee
(including, without limitation, the delivery of investment representation
letters and legal opinions reasonably satisfactory to the Company). The Company
shall not require Holder to provide an opinion of counsel if the transfer is to
an affiliate of Holder or if there is no material question as to the
availability of current information as referenced in Rule 144(c), Holder
represents that it has complied with Rule 144(d) and (e) in reasonable detail,
the selling broker represents that it has complied with Rule 144(f), and the
Company is provided with a copy of Holder's notice of proposed sale.

                                        3
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     4.4     TRANSFER PROCEDURE. Subject to the provisions of Section 4.3,
Holder may transfer all or part of this warrant or the Shares issuable upon
exercise of this warrant (or the securities issuable, directly or indirectly,
upon conversion of the Shares, if any) by giving the Company notice of the
portion of the warrant being transferred setting forth the name, address and
taxpayer identification number of the transferee and surrendering this warrant
to the Company for reissuance to the transferee(s) (and Holder, if applicable);
PROVIDED, HOWEVER, that Holder may transfer all or part of this warrant to its
affiliates at any time without notice to the Company, and such affiliate shall
then be entitled to all the rights of Holder under this warrant and any related
agreements, and the Company shall cooperate fully in ensuring that any stock
issued upon exercise of this warrant is issued in the name of the affiliate that
exercises the warrant. The terms and conditions of this warrant shall inure to
the benefit of, and be binding upon, the Company and the holders hereof and
their respective permitted successors and assigns. The Company shall have the
right to refuse to transfer any portion of this warrant to any person who
directly competes with the Company, unless the Company is filing financial
information with the SEC pursuant to the Securities Exchange Act of 1934.

     4.5     NOTICES. All notices and other communications from the Company to
the Holder, or vice versa, shall be deemed delivered and effective when given
personally or mailed by first-class registered or certified mail, postage
prepaid, at such address as may have been furnished to the Company or the
Holder, as the case may be, in writing by the Company or such Holder from time
to time. All notices to the Holder shall be addressed as follows:

                            Rockport Venture Securities, LLC
                            63 Main Street
                            Gloucester, MA 01936
                            Attention: Manager

     4.6     WAIVER. This warrant and any term hereof may be changed, waived,
discharged or terminated only by an instrument in writing signed by the party
against which enforcement of such change, waiver, discharge or termination is
sought.

     4.7     ATTORNEYS' FEES. In the event of any dispute between the parties
concerning the terms and provisions of this warrant, the party prevailing in
such dispute shall be entitled to collect from the other party all costs
incurred in such dispute, including reasonable attorneys' fees.

     4.8     GOVERNING LAW. This warrant shall be governed by and construed in
accordance with the laws of the Commonwealth of Massachusetts, without giving
effect to its principles regarding conflicts of law.


                            COMBINATORX, INCORPORATED


                            By: /s/ Edward Davis
                               -------------------------------------------------
                            Edward Davis
                            Executive Vice President and Chief Financial Officer
                            Hereunto Duly Authorized

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                                   APPENDIX 1

                               NOTICE OF EXERCISE

     1.   The undersigned hereby elects to purchase ___________ shares of
the ___________ stock of COMBINATORX, INCORPORATED pursuant to the terms of
the attached warrant, and tenders herewith payment of the purchase price of such
shares in full.

     2.   The undersigned hereby elects to convert the attached warrant into
shares in the manner specified in Section 1.2 of the warrant. This conversion is
exercised with respect to ___________ of the shares covered by the warrant.

     [STRIKE WHICHEVER OF PARAGRAPH 1 OR 2 THAT DOES NOT APPLY.]

     3.   Please issue a certificate or certificates representing said shares in
the name of the undersigned or in such other name as is specified below:

          Rockport Venture Securities, LLC
          63 Main Street
          Gloucester, MA 01936
          Attention: Manager

          OR Registered Assignee

          Name: ___________________

          Address: ________________

          _________________________

     4.   The undersigned represents it is acquiring the shares solely for its
own account and not as a nominee for any other party and not with a view toward
the resale or distribution thereof except in compliance with applicable
securities laws.

ROCKPORT VENTURE SECURITIES, LLC
or Registered Assignee



___________________________________
(Signature)


___________________________________
 (Date)

                                        5
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                                    EXHIBIT A

                            ANTI-DILUTION ADJUSTMENTS

(i)  If the corporation shall issue, after the "Issue Date" as set forth at
the top of the first page of this warrant (the "Original Purchase Date"), any
Additional Stock (as defined below in section (ii)) without consideration or for
a consideration per share less than the Warrant Price in effect immediately
prior to the issuance of such Additional Stock, the Warrant Price in effect
immediately prior to each such issuance shall forthwith (except as otherwise
provided in this clause (i)) be adjusted to a price determined by multiplying
such Warrant Price by a fraction, the numerator of which shall be the number of
shares of Common Stock outstanding immediately prior to such issuance plus the
number of shares of Common Stock which the aggregate consideration received by
the corporation for the total number of shares of Additional Stock so issued
would purchase at such Warrant Price in effect immediately prior to such
issuance, and the denominator of which shall be the number of shares of Common
Stock outstanding immediately prior to such issuance plus the number of shares
of such Additional Stock so issued. For the purpose of the above calculation,
the number of shares of Common Stock outstanding immediately prior to such
issuance shall be calculated on a fully diluted basis, as if all shares of
convertible Preferred Stock and all vested securities convertible into or
exchangeable for Common Stock at such time had been fully converted into or
exchanged for shares of Common Stock immediately prior to such issuance as of
such date.

     (A)  No adjustment of the Warrant Price shall be made in an amount less
     than one cent per share, PROVIDED that any adjustments which are not
     required to be made by reason of this sentence shall be carried forward and
     shall be either taken into account in any subsequent adjustment made prior
     to three (3) years from the date of the event giving rise to the adjustment
     being carried forward, or shall be made at the end of three (3) years from
     the date of the event giving rise to the adjustment being carried forward.
     Except to the limited extent provided for in subsections (B)(4) and (B)(5),
     no adjustment of such Warrant Price pursuant to this Section (i) shall have
     the effect of increasing the Warrant Price above the Warrant Price in
     effect immediately prior to such adjustment.

     (B)  For purposes of determining whether any Additional Stock (as defined
     below) was issued for consideration less than the Warrant Price pursuant to
     Section (i), the consideration deemed received by the corporation for the
     issue of any Additional Shares (as defined below) of Common Stock shall be
     computed as follows:

          (1)  CASH AND PROPERTY: Such consideration shall:

               (I)   insofar as it consists of cash, be computed at the
               aggregate amount of cash received by the corporation, excluding
               amounts paid or payable for accrued interest;

               (II)  insofar as it consists of property other than cash, be
               computed at the fair market value thereof at the time of such
               issue, as determined in good faith by the Board of Directors of
               the corporation; and

               (III) in the event Additional Shares (as defined below) of
               Common Stock are issued together with other shares or securities
               or other assets of the corporation for consideration which covers
               both, be the proportion of such consideration so received,
               computed as provided in clauses (I) and (II) above, as determined
               in good faith by the Board of Directors of the Corporation.

          (2)  OPTIONS AND CONVERTIBLE SECURITIES. The consideration per
          share received by the corporation for Additional Shares (as defined
          below) of Common Stock deemed to have been issued pursuant to Section
          (i)(B)(3), relating to options to purchase or rights to subscribe for
          Common Stock or securities convertible into or exchangeable for Common
          Stock, shall be determined by dividing

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               (I)   the total amount, if any, received or receivable by the
               corporation as consideration for the issue of such options to
               purchase or rights to subscribe for Common Stock or securities
               convertible into or exchangeable for Common Stock, plus the
               minimum aggregate amount of additional consideration (as set
               forth in the instruments relating thereto, without regard to any
               provision contained therein for a subsequent adjustment of such
               consideration) payable to the corporation upon the exercise of
               such options to purchase Common Stock or the conversion or
               exchange of such convertible securities for Common Stock, or in
               the case of options for convertible securities that may be
               converted into Common Stock, the exercise of such options for
               such convertible securities and the conversion or exchange of
               such convertible securities, by

               (II)  the maximum number of shares of Common Stock (as set forth
               in the instruments relating thereto, without regard to any
               provision contained therein for a subsequent adjustment of such
               number) issuable upon the exercise of such options to purchase or
               rights to subscribe for Common Stock or securities convertible
               into or exchangeable for Common Stock.

          (3)  If the corporation at any time or from time to time after the
          Original Purchase Date shall issue any options to purchase or rights
          to subscribe for Common Stock or securities convertible into or
          exchangeable for Common Stock (excluding options to purchase or rights
          to subscribe for Common Stock or securities convertible into or
          exchangeable for Common Stock which, upon exercise, conversion or
          exchange thereof, would entitle the holder thereof to receive shares
          of Common Stock which are specifically excepted from the definition of
          Additional Shares of Common Stock by Section (ii) below) or shall fix
          a record date for the determination of holders of any class of
          securities entitled to receive any such options to purchase or rights
          to subscribe for Common Stock or securities convertible into or
          exchangeable for Common Stock, then the maximum number of shares of
          Common Stock (as set forth in the instrument relating thereto without
          regard to any provision contained therein for a subsequent adjustment
          of such number) issuable upon the exercise of such options to purchase
          or rights to subscribe for Common Stock or, in the case of options to
          purchase or rights to subscribe for Common Stock or securities
          convertible into or exchangeable for Common Stock therefor, the
          conversion or exchange of such securities convertible into or
          exchangeable for Common Stock, shall be deemed to be Additional Stock
          issued as of the time of such issue or, in case such a record date
          shall have been fixed, as of the close of business on such record
          date.

          (4)  In the event of any change in the number of shares of Common
          Stock deliverable or in the consideration payable to this corporation
          upon exercise of such options to purchase or rights to subscribe for
          Common Stock or securities convertible into or exchangeable for Common
          Stock, Including, but not limited to, a change resulting from the
          antidilution provisions thereof, the Warrant Price, to the extent in
          any way affected by or computed using such options, rights or
          securities, shall be recomputed to reflect such change, but no further
          adjustment shall be made for the actual issuance of Common Stock or
          any payment of such consideration upon the exercise of any such
          options or rights or the conversion or exchange of such securities.

          (5)  Upon the expiration of any such options or rights, the
          termination of any such rights to convert or exchange or the
          expiration of any options or rights related to such convertible or
          exchangeable securities, the Warrant Price, to the extent in any way
          affected by or computed using such options, rights or securities or
          options or rights related to such securities, shall be recomputed to
          reflect the issuance of only the number of shares of Common Stock (and
          convertible or exchangeable securities which remain in effect)
          actually issued upon the exercise of such options or rights, upon the
          conversion or exchange of such securities or upon the exercise of the
          options or rights related to such securities.

          (6)  The number of shares of Common Stock deemed issued and the
          consideration deemed paid therefor pursuant to Sections (i)(B) shall
          be appropriately adjusted to reflect any change, termination or
          expiration of the type described in either Section (i)(B)(4) or (5).

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          (G)  the issuance of shares of capital stock of the Company in
          connection with any strategic alliances or strategic licensing
          agreements approved by the Board of Directors including the
          affirmative vote of the member of the Board of Directors appointed
          solely by the holders of Series C Preferred Stock;

          (H)  shares of Common Stock issued upon conversion of the Series
          Preferred Stock; and

          (I)  shares of Common Stock issued or issuable in a public
          offering before or in connection with which all outstanding shares of
          Series Preferred Stock will be converted to Common Stock.

END OF EXHIBIT A

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