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                                                         Exhibit 10.11


                        Schedule of Warrantholders



Warrantholder
-------------
Lighthouse Capital Partners IV, L.P.
Lighthouse Capital Partners V, L.P.




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THIS WARRANT HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS
AMENDED (THE "1933 ACT"), OR ANY APPLICABLE STATE SECURITIES LAWS, AND MAY NOT
BE SOLD OR TRANSFERRED UNLESS SUCH SALE OR TRANSFER IS IN ACCORDANCE WITH THE
REGISTRATION REQUIREMENTS OF SUCH ACT AND APPLICABLE LAWS OR SOME OTHER
EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF SUCH ACT AND APPLICABLE LAWS IS
AVAILABLE WITH RESPECT THERETO.


                        PREFERRED STOCK PURCHASE WARRANT


Warrant No._________     Number of Shares: Calculated under Section 2(a) and (b)
                                           Series D Convertible Preferred Stock


                            COMBINATORX, INCORPORATED


                        Effective as of September 7, 2004

                          Void after September 7, 2011


      1.    ISSUANCE. This Preferred Stock Purchase Warrant (the "WARRANT") is
issued to _________________________________ by COMBINATORX, INCORPORATED, a
Delaware corporation (hereinafter with its successors called the "COMPANY").

      2.    PURCHASE PRICE; NUMBER OF SHARES.

      (a)   The registered holder of this Warrant (the "HOLDER"), commencing
on the date hereof, is entitled upon surrender of this Warrant with the
subscription form annexed hereto duly executed, at the principal office of
the Company, to purchase from the Company, at a price per share of $3.8558
(the "PURCHASE PRICE"), 45,386 fully paid and nonassessable shares of the
Company's Series D Convertible Preferred Stock (the "EXERCISE QUANTITY"),
$0.001 par value per share (the "PREFERRED STOCK").

      (b)   The Exercise Quantity shall automatically increase by an amount
equal to (x) 1.625% of the Aggregate Advances made under the Loan Agreement,
divided by (y) the Purchase Price.

In addition to other terms which may be defined herein, the following terms, as
used in this Warrant, shall have the following meanings:

            (i)   "Aggregate Advances" means the aggregate principal dollar
      amount of all Advances made under the Loan Agreement, whether such
      Advances are outstanding or prepaid, at the time of any adjustment to the
      Exercise Quantity.

            (ii)  "Loan Agreement" means that certain Loan and Security
      Agreement No. 4201 dated September 7, 2004 between the Company and
      Lighthouse Capital Partners V, L.P.

Any term not defined herein shall have the meaning as set forth in the Loan
Agreement.

Until such time as this Warrant is exercised in full or expires, the Purchase
Price and the securities issuable upon exercise of this Warrant are subject to
adjustment as hereinafter provided. The person or persons in whose name or names
any certificate representing shares of Preferred Stock is issued hereunder shall
be deemed to have become the holder of record of the shares represented thereby
as at the close of business on the date this Warrant is exercised with respect
to such shares, whether or not the transfer books of the Company shall be
closed.


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      3.    PAYMENT OF PURCHASE PRICE. The Purchase Price may be paid (i) in
cash or by check, (ii) by the surrender by the Holder to the Company of any
promissory notes or other obligations issued by the Company, with all such notes
and obligations so surrendered being credited against the Purchase Price in an
amount equal to the principal amount thereof plus accrued interest to the date
of surrender, or (iii) by any combination of the foregoing.

      4.    NET ISSUE ELECTION. The Holder may elect to receive, without the
payment by the Holder of any additional consideration, shares of Preferred Stock
equal to the value of this Warrant or any portion hereof by the surrender of
this Warrant or such portion to the Company, with the net issue election notice
annexed hereto duly executed, at the principal office of the Company. Thereupon,
the Company shall issue to the Holder such number of fully paid and
nonassessable shares of Preferred Stock as is computed using the following
formula:

                                   X=Y(A-B)
                                     ------
                                        A

     where: X =   the number of shares of Preferred Stock to be issued to the
                  Holder pursuant to this SECTION 4.

            Y =   the number of shares of Preferred Stock covered by this
                  Warrant in respect of which the net issue election is made
                  pursuant to this SECTION 4.

            A =   the Fair Market Value (defined below) of one share of
                  Preferred Stock, as determined at the time the net issue
                  election is made pursuant to this SECTION 4.

            B =   the Purchase Price in effect under this Warrant at the time
                  the net issue election is made pursuant to this SECTION 4.

            "FAIR MARKER VALUE" of a share of Preferred Stock (or fully paid and
nonassessable shares of the Company's common stock, $0.001 par value (the
"COMMON STOCK") if the Preferred Stock has been automatically converted into
Common Stock) as of the date that the net issue election is made (the
"DETERMINATION DATE") shall mean:

            (i)   If the net issue election is made in connection with and
contingent upon the closing of the sale of the Company's Common Stock to the
public in a public offering pursuant to a Registration Statement under the 1933
Act (a "PUBLIC OFFERING"), and if the Company's Registration Statement relating
to such Public Offering ("REGISTRATION STATEMENT") has been declared effective
by the Securities and Exchange Commission, then the initial "Price to Public"
specified in the final prospectus with respect to such offering multiplied by
the number of shares of Common Stock into which each share of Preferred Stock is
then convertible.

            (ii)  If the net issue election is not made in connection with and
contingent upon a Public Offering, then as follows:

                  (a)   If traded on a securities exchange or the Nasdaq
National Market, the fair market value of the Common Stock shall be deemed to be
the average of the closing or last reported sale prices of the Common Stock on
such exchange or market over the five day period ending five trading days prior
to the Determination Date, and the fair market value of the Preferred Stock
shall be deemed to be such fair market value of the Common Stock multiplied by
the number of shares of Common Stock into which each share of Preferred Stock is
then convertible;

                  (b)   If otherwise traded in an over-the-counter market, the
fair market value of the Common Stock shall be deemed to be the average of the
closing ask prices of the Common Stock over the five day period ending five
trading days prior to the Determination Date, and the fair market value of the
Preferred Stock shall be deemed to be such fair market value of the Common Stock
multiplied by the number of shares of Common Stock into which each share of
Preferred Stock is then convertible; and


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                  (c)   If there is no public market for the Common Stock, then
fair market value shall be determined in good faith by the Company's Board of
Directors.

      5.    PARTIAL EXERCISE. This Warrant may be exercised in part, and the
Holder shall be entitled to receive a new warrant, which shall be dated as of
the date of this Warrant, covering the number of shares in respect of which this
Warrant shall not have been exercised.

      6.    FRACTIONAL SHARES. In no event shall any fractional share of
Preferred Stock be issued upon any exercise of this Warrant. If, upon exercise
of this Warrant in its entirety, the Holder would, except as provided in this
SECTION 6, be entitled to receive a fractional share of Preferred Stock, then
the Company shall pay the Holder an amount in cash equal to the value of such
fractional share.

      7.    EXPIRATION DATE; AUTOMATIC EXERCISE. This Warrant shall expire on
the close of business on September 7, 2011 (the "EXPIRATION DATE") and shall be
void thereafter.

Notwithstanding the foregoing, this Warrant shall automatically be deemed to be
exercised in full pursuant to the provisions of SECTION 4 hereof, without any
further action on behalf of the Holder, immediately prior to the time this
Warrant would otherwise expire pursuant to this SECTION 7.

      8.    RESERVED SHARES; VALID ISSUANCE. The Company covenants that it will
at all times from and after the date hereof reserve and keep available such
number of its authorized shares of Preferred Stock and Common Stock free from
all preemptive or similar rights therein, as will be sufficient to permit,
respectively, the exercise of this Warrant in full and the conversion into
shares of Common Stock of all shares of Preferred Stock receivable upon such
exercise. The Company further covenants that such shares as may be issued
pursuant to such exercise and/or conversion will, upon issuance, be duly and
validly issued, fully paid and nonassessable and free from all taxes, liens and
charges with respect to the issuance thereof.

      9.    STOCK SPLITS AND DIVIDENDS. If after the date hereof the Company
shall subdivide the Preferred Stock, by split-up or otherwise, or combine the
Preferred Stock, or issue additional shares of Preferred Stock in payment of a
stock dividend on the Preferred Stock, the number of shares of Preferred Stock
issuable on the exercise of this Warrant shall forthwith be proportionately
increased in the case of a subdivision or stock dividend, or proportionately
decreased in the case of a combination, and the Purchase Price shall forthwith
be proportionately decreased in the case of a subdivision or stock dividend, or
proportionately increased in the case of a combination.

      10.   ADJUSTMENTS FOR DILUTING ISSUANCES. The other antidilution rights
applicable to the Preferred Stock and the Common Stock of the Company are set
forth in the Amended and Restated Certificate of Incorporation, as amended from
time to time (the "CERTIFICATE"), a true and complete copy in its current form
which is attached hereto as EXHIBIT A. Such rights shall not be restated,
amended or modified in any manner which affects the Holder differently than the
holders of Series D Preferred without such Holder's prior written consent. The
Company shall promptly provide the Holder hereof with any restatement, amendment
or modification to the Certificate promptly after the same has been made.

      11.   MERGERS AND RECLASSIFICATIONS. If after the date hereof the Company
shall enter into any Reorganization (as hereinafter defined), then, as a
condition of such Reorganization, lawful provisions shall be made, and duly
executed documents evidencing the same from the Company or its successor shall
be delivered to the Holder, so that the Holder shall thereafter have the right
to purchase, at a total price not to exceed that payable upon the exercise of
this Warrant in full, the kind and amount of shares of stock and other
securities and property receivable upon such Reorganization by a holder of the
number of shares of Preferred Stock which might have been purchased by the
Holder immediately prior to such Reorganization, and in any such case
appropriate provisions shall be made with respect to the rights and interest of
the Holder to the end that the provisions hereof (including without limitation,
provisions for the adjustment of the Purchase Price and the number of shares
issuable hereunder and the provisions relating to the net issue election) shall
thereafter be applicable in relation to any shares of stock or other securities
and property thereafter deliverable upon exercise hereof. For the purposes of
this SECTION 11, the term "REORGANIZATION" shall include without limitation any
reclassification, capital reorganization or change of the


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Preferred Stock (other than as a result of a subdivision, combination or stock
dividend provided for in SECTION 9 hereof), or any consolidation of the Company
with, or merger of the Company into, another corporation or other business
organization (other than a merger in which the Company is the surviving
corporation and which does not result in any reclassification or change of the
outstanding Preferred Stock), or any sale or conveyance to another corporation
or other business organization of all or substantially all of the assets of the
Company.

      12.   CERTIFICATE OF ADJUSTMENT. Whenever the Purchase Price is adjusted,
as herein provided, the Company shall promptly deliver to the Holder a
certificate of the Company's chief financial officer setting forth the Purchase
Price after such adjustment and setting forth a brief statement of the facts
requiring such adjustment.

      13.   NOTICES OF RECORD DATE, ETC. In the event of:

            (a)   any taking by the Company of a record of the holders of any
class of securities for the purpose of determining the holders thereof who are
entitled to receive any dividend or other distribution, or any right to
subscribe for, purchase, sell or otherwise acquire or dispose of any shares of
stock of any class or any other securities or property, or to receive any other
right;

            (b)   any reclassification of the capital stock of the Company,
capital reorganization of the Company, consolidation or merger involving the
Company, or sale or conveyance of all or substantially all of its assets; or

            (c)   any voluntary or involuntary dissolution, liquidation or
winding-up of the Company;

then in each such event the Company will provide or cause to be provided to the
Holder a written notice thereof. Such notice shall be provided at least twenty
(20) business days prior to the date specified in such notice on which any such
action is to be taken or such lesser notice period as is provided to the
Company's Preferred Stock holders in connection with such action.

      14.   REPRESENTATIONS, WARRANTIES AND COVENANTS. This Warrant is issued
and delivered by the Company and accepted by each Holder on the basis of the
following representations, warranties and covenants made by the Company:

            (a)   The Company has all necessary authority to issue, execute and
deliver this Warrant and to perform its obligations hereunder. This Warrant has
been duly authorized issued, executed and delivered by the Company and is the
valid and binding obligation of the Company, enforceable in accordance with its
terms.

            (b)   The shares of Preferred Stock issuable upon the exercise of
this Warrant have been duly authorized and reserved for issuance by the Company
and, when issued in accordance with the terms hereof, will be validly issued,
fully paid and nonassessable.

            (c)   The issuance, execution and delivery of this Warrant do not,
and the issuance of the shares of Preferred Stock upon the exercise of this
Warrant in accordance with the terms hereof will not, (i) violate or contravene
the Company's Certificate or by-laws, or any law, statute, regulation, rule,
judgment or order applicable to the Company, (ii) violate, contravene or result
in a breach or default under any contract, agreement or instrument to which the
Company is a party or by which the Company or any of its assets are bound or
(iii) require the consent or approval of or the filing of any notice or
registration with any person or entity.

            (d)   As long as this Warrant is, or any shares of Preferred Stock
issued upon exercise of this Warrant or any shares of Common Stock issued upon
conversion of such shares of Preferred Stock are, issued and outstanding, the
Company will provide to the Holder the financial and other information as
further described in the Loan Agreement.

            (e)   So long as this Warrant has not terminated, Holder shall be
entitled to receive such financial and other information as the Holder would be
entitled to receive under the Stock Purchase Agreement


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applicable to the Preferred Stock if Holder were a holder of that number of
shares issuable upon full exercise of this Warrant.

            (f)   As of the date hereof, the authorized capital stock of the
Company consists of (i) 29,000,000 shares of Common Stock, of which 4,051,843
shares are issued and outstanding and 87,530 shares are reserved for issuance
upon the exercise of this Warrant with respect to Common Stock and the
conversion of the Preferred Stock into Common Stock if this Warrant is exercised
with respect to Preferred Stock, and (ii) 606,792 shares of Series A Preferred
Stock, of which 606,792 are issued and outstanding shares and (iii) 3,364,250
shares of Series B Preferred Stock, of which 3,364,250 are issued and
outstanding shares (iv) 10,795,666 shares of Series C Preferred Stock, of which
10,795,666 are issued and outstanding shares (v) 8,493,320 shares of Series D
Preferred Stock, of which ) 8,292,699 are issued and outstanding shares.
Attached hereto as EXHIBIT B is a capitalization table summarizing the
capitalization of the Company. Once per calendar quarter, the Company will
provide Holder with a current capitalization table indicating changes, if any,
to the number of outstanding shares of common stock and preferred stock.

      15.   REGISTRATION RIGHTS. The Company grants to the Holder all the rights
of a "Holder" under the Company's Second Amended and Restated Investors' Rights
Agreement dated as of February 18, 2004 (the "RIGHTS AGREEMENT"), including,
without limitation, the registration rights contained therein, and agrees to
amend the Rights Agreement so that (i) the shares of Common Stock issuable upon
conversion of the shares of Preferred Stock issuable upon exercise of this
Warrant shall be "REGISTRABLE SECURITIES," and (ii) the Holder shall be a
"Holder" for all purposes of such Rights Agreement.

      16.   AMENDMENT. The terms of this Warrant may be amended, modified or
waived only with the written consent of the Company and the Holder.

      17.   REPRESENTATIONS AND COVENANTS OF THE HOLDER. This Warrant has been
entered into by the Company in reliance upon the following representations and
covenants of the Holder, which by its execution hereof the Holder hereby
confirms:

            (a)   INVESTMENT PURPOSE. The right to acquire Preferred Stock or
the Preferred Stock issuable upon exercise of the Holder's rights contained
herein will be acquired for investment and not with a view to the sale or
distribution of any part thereof, and the Holder has no present intention of
selling or engaging in any public distribution of the same except pursuant to a
registration or exemption.

            (b)   ACCREDITED INVESTOR. Holder is an "accredited investor" within
the meaning of the Securities and Exchange Rule 501 of Regulation D, as
presently in effect.

            (c)   PRIVATE ISSUE. The Holder understands (i) that the Preferred
Stock issuable upon exercise of the Holder's rights contained herein is not
registered under the 1933 Act or qualified under applicable state securities
laws on the ground that the issuance contemplated by this Warrant will be exempt
from the registration and qualifications requirements thereof, and (ii) that the
Company's reliance on such exemption is predicated on the representations set
forth in this SECTION 17.

            (d)   FINANCIAL RISK. The Holder has such knowledge and experience
in financial and business matters as to be capable of evaluating the merits and
risks of its investment and has the ability to bear the economic risks of its
investment.

      18.   NOTICES, TRANSFERS, ETC.

            (a)   Any notice or written communication required or permitted to
be given to the Holder may be given by certified mail or delivered to the Holder
at the address most recently provided by the Holder to the Company.


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            (b)   Subject to compliance with applicable federal and state
securities laws, this Warrant may be transferred by the Holder with respect to
any or all of the shares purchasable hereunder. Upon surrender of this Warrant
to the Company, together with the assignment notice annexed hereto duly
executed, for transfer of this Warrant as an entirety by the Holder, the Company
shall issue a new warrant of the same denomination to the assignee. Upon
surrender of this Warrant to the Company, together with the assignment hereof
properly endorsed, by the Holder for transfer with respect to a portion of the
shares of Preferred Stock purchasable hereunder, the Company shall issue a new
warrant to the assignee, in such denomination as shall be requested by the
Holder hereof, and shall issue to such Holder a new warrant covering the number
of shares in respect of which this Warrant shall not have been transferred.

            (c)   In case this Warrant shall be mutilated, lost, stolen or
destroyed, the Company shall issue a new warrant of like tenor and denomination
and deliver the same (i) in exchange and substitution for and upon surrender and
cancellation of any mutilated Warrant, or (ii) in lieu of any Warrant lost,
stolen or destroyed, upon receipt of an affidavit of the Holder or other
evidence reasonably satisfactory to the Company of the loss, theft or
destruction of such Warrant.

      19.   NO IMPAIRMENT. The Company will not, by amendment of its Certificate
or through any reclassification, capital reorganization, consolidation, merger,
sale or conveyance of assets, dissolution, liquidation, issue or sale of
securities or any other voluntary action, avoid or seek to avoid the observance
of performance of any of the terms of this Warrant, but will at all times in
good faith assist in the carrying out of all such terms and in the taking of all
such action as may be necessary or appropriate in order to protect the rights of
the Holder.

      20.   GOVERNING LAW. The provisions and terms of this Warrant shall be
governed by and construed in accordance with the internal laws of the State of
Delaware without giving effect to its principles regarding conflicts of laws.

      21.   SUCCESSORS AND ASSIGNS. This Warrant shall be binding upon the
Company's successors and assigns and shall inure to the benefit of the Holder's
successors, legal representatives and permitted assigns.

      22.   BUSINESS DAYS. If the last or appointed day for the taking of any
action required or the expiration of any rights granted herein shall be a
Saturday or Sunday or a legal holiday in California, then such action may be
taken or right may be exercised on the next succeeding day which is not a
Saturday or Sunday or such a legal holiday.

      23.   QUALIFYING PUBLIC OFFERING. If the Company shall effect a firm
commitment underwritten public offering of shares of Common Stock which results
in the conversion of the Preferred Stock into Common Stock pursuant to the
Company's Certificate in effect immediately prior to such offering, then,
effective upon such conversion, this Warrant shall change from the right to
purchase shares of Preferred Stock to the right to purchase shares of Common
Stock, and the Holder shall thereupon have the right to purchase, at a total
price equal to that payable upon the exercise of this Warrant in full, the
number of shares of Common Stock which would have been receivable by the Holder
upon the exercise of this Warrant for shares of Preferred Stock immediately
prior to such conversion of such shares of Preferred Stock into shares of Common
Stock, and in such event appropriate provisions shall be made with respect to
the rights and interest of the Holder to the end that the provisions hereof
(including, without limitation, the provisions for the adjustment of the
Purchase Price and of the number of shares purchasable upon exercise of this
Warrant and the provisions relating to the net issue election) shall thereafter
be applicable to any shares of Common Stock deliverable upon the exercise
hereof.


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      24.   VALUE. The Company and the Holder agree that the value of this
Warrant on the date of grant is $50.

                                  COMBINATORX, INCORPORATED


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

                                  Name:
                                       ----------------------------

                                  Title:
                                        ---------------------------


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