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                                                                 Exhibit 10.13

   NEITHER THIS PROMISSORY NOTE NOR THE MASTER SECURITY AGREEMENT TO WHICH THIS
   NOTE IS TIED HAVE BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS
   AMENDED. NO SALE OR DISPOSITION MAY BE EFFECTED EXCEPT IN COMPLIANCE WITH
   RULE 144 UNDER SAID ACT OR WITHOUT AN EFFECTIVE REGISTRATION STATEMENT
   RELATED THERETO OR AN OPINION OF COUNSEL FOR THE HOLDER, SATISFACTORY TO THE
   COMPANY, THAT SUCH REGISTRATION IS NOT REQUIRED UNDER THE ACT OR RECEIPT OF A
   NO-ACTION LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION

                                 PROMISSORY NOTE

                               -------------------
                                     (DATE)

   FOR VALUE RECEIVED, COMBINATORX, INCORPORATED a corporation located at the
address stated below ("MAKER") promises, jointly and severally if more than one,
to pay to the order of GENERAL ELECTRIC CAPITAL CORPORATION or any subsequent
holder hereof (each, a "PAYEE") at its office located at 83 WOOSTER HEIGHTS
ROAD, DANBURY, CT 06810 or at such other place as Payee or the holder hereof may
designate, the principal sum THREE MILLION AND 00/100 DOLLARS ($3,000,000.00),
with interest on the unpaid principal balance, from the date hereof through and
including the dates of payment, at a fixed interest rate of Eight and Forty-Two
Hundredths percent (8.42%) per annum, to be paid in lawful money of the United
States, in Thirty-Six (36) consecutive monthly installments of principal and
interest as follows:

<Table>
<Caption>
           Periodic
          Installment                                Amount
        --------------------------------------------------------
        <S>                                          <C>
        Thirty-Five (35)                             $ 94,591.44
</Table>

   each ("Periodic Installment") and a final installment which shall be in the
   amount of the total outstanding principal and interest. The first Periodic
   Installment shall be due and payable on ________ and the following Periodic
   Installments and the final installment shall be due and payable on the same
   day of each succeeding month (each, a "Payment Date"). Such installments have
   been calculated on the basis of a 360 day year of twelve 30-day months. Each
   payment may, at the option of the Payee, be calculated and applied on an
   assumption that such payment would be made on its due date.

   The acceptance by Payee of any payment which is less than payment in full of
   all amounts due and owing at such time shall not constitute a waiver of
   Payee's right to receive payment in full at such time or at any prior or
   subsequent time.

   The Maker hereby expressly authorizes the Payee to insert the date value is
   actually given in the blank space on the face hereof and on all related
   documents pertaining hereto.

   This Note may be secured by a security agreement, chattel mortgage, pledge
   agreement or like instrument (each of which is hereinafter called a "SECURITY
   AGREEMENT").

   Time is of the essence hereof. If any installment or any other sum due under
   this Note or any Security Agreement is not received within ten (10) days
   after its due date, the Maker agrees to pay, in addition to the amount of
   each such installment or other sum, a late payment charge of five percent
   (5%) of the amount of said installment or other sum, but not exceeding any
   lawful maximum. If (i) Maker fails to make payment of any amount due
   hereunder within ten (10) days after the same becomes

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   due and payable; or (ii) Maker is in default under, or fails to perform under
   any term or condition contained in any Security Agreement after ten (10) days
   written notice, then the entire principal sum remaining unpaid, together with
   all accrued interest thereon and any other sum payable under this Note or any
   Security Agreement, at the election of Payee, shall immediately become due
   and payable, with interest thereon at the lesser of eighteen percent (18%)
   per annum or the highest rate not prohibited by applicable law from the date
   of such accelerated maturity until paid (both before and after any judgment).

   The Maker may prepay in full, but not in part, its entire indebtedness
   hereunder upon payment of the outstanding principal amount plus all accrued
   interest to the date of prepayment, plus an additional sum as a premium equal
   to the following percentages of the remaining principal balance for the
   indicated period
   Months 1 - 12: No Prepayment Allowed
   Months 13 - 24: 6% premium
   Months 25 - 36: 5% premium

   It is the intention of the parties hereto to comply with the applicable usury
   laws; accordingly, it is agreed that, notwithstanding any provision to the
   contrary in this Note or any Security Agreement, in no event shall this Note
   or any Security Agreement require the payment or permit the collection of
   interest in excess of the maximum amount permitted by applicable law. If any
   such excess interest is contracted for, charged or received under this Note
   or any Security Agreement, or if all of the principal balance shall be
   prepaid, so that under any of such circumstances the amount of interest
   contracted for, charged or received under this Note or any Security Agreement
   on the principal balance shall exceed the maximum amount of interest
   permitted by applicable law, then in such event (a) the provisions of this
   paragraph shall govern and control, (b) neither Maker nor any other person or
   entity now or hereafter liable for the payment hereof shall be obligated to
   pay the amount of such interest to the extent that it is in excess of the
   maximum amount of interest permitted by applicable law, (c) any such excess
   which may have been collected shall be either applied as a credit against the
   then unpaid principal balance or refunded to Maker, at the option of the
   Payee, and (d) the effective rate of interest shall be automatically reduced
   to the maximum lawful contract rate allowed under applicable law as now or
   hereafter construed by the courts having jurisdiction thereof. It is further
   agreed that without limitation of the foregoing, all calculations of the rate
   of interest contracted for, charged or received under this Note or any
   Security Agreement which are made for the purpose of determining whether such
   rate exceeds the maximum lawful contract rate, shall be made, to the extent
   permitted by applicable law, by amortizing, prorating, allocating and
   spreading in equal parts during the period of the full stated term of the
   indebtedness evidenced hereby, all interest at any time contracted for,
   charged or received from Maker or otherwise by Payee in connection with such
   indebtedness; provided, however, that if any applicable state law is amended
   or the law of the United States of America preempts any applicable state law,
   so that it becomes lawful for the Payee to receive a greater interest per
   annum rate than is presently allowed, the Maker agrees that, on the effective
   date of such amendment or preemption, as the case may be, the lawful maximum
   hereunder shall be increased to the maximum interest per annum rate allowed
   by the amended state law or the law of the United States of America.

   The Maker and all sureties, endorsers, guarantors or any others (each such
   person, other than the Maker, an "OBLIGOR") who may at any time become liable
   for the payment hereof jointly and severally consent hereby to any and all
   extensions of time, renewals, waivers or modifications of, and all
   substitutions or releases of, security or of any party primarily or
   secondarily liable on this Note or any Security Agreement or any term and
   provision of either, which may be made, granted or consented to by Payee, and
   agree that suit may be brought and maintained against any one or more of
   them, at the election of Payee without joinder of any other as a party
   thereto, and that Payee shall not be required first to foreclose, proceed
   against, or exhaust any security hereof in order to enforce payment of this
   Note. The Maker and each Obligor hereby waives presentment, demand for
   payment, notice of nonpayment, protest, notice of protest, notice of
   dishonor, and all other notices in connection herewith, as well as filing of
   suit (if permitted by law) and diligence in collecting this Note or enforcing
   any of the security hereof, and agrees to pay (if permitted by law) all
   expenses incurred in collection, including Payee's actual attorneys' fees.
   Maker and each Obligor agrees that fees not in excess of twenty percent (20%)
   of the amount then due shall be deemed reasonable.

   THE MAKER HEREBY UNCONDITIONALLY WAIVES ITS RIGHTS TO A JURY TRIAL OF ANY
   CLAIM OR CAUSE OF ACTION BASED UPON OR ARISING OUT OF, DIRECTLY OR
   INDIRECTLY, THIS NOTE, ANY OF THE RELATED DOCUMENTS, ANY DEALINGS BETWEEN
   MAKER AND PAYEE RELATING TO THE SUBJECT MATTER OF THIS TRANSACTION OR ANY
   RELATED TRANSACTIONS, AND/OR THE RELATIONSHIP THAT IS BEING ESTABLISHED
   BETWEEN MAKER AND PAYEE. THE SCOPE OF THIS WAIVER IS INTENDED TO BE ALL
   ENCOMPASSING OF ANY AND ALL DISPUTES THAT MAY BE FILED IN

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   ANY COURT (INCLUDING, WITHOUT LIMITATION, CONTRACT CLAIMS, TORT CLAIMS,
   BREACH OF DUTY CLAIMS, AND ALL OTHER COMMON LAW AND STATUTORY CLAIMS.) THIS
   WAIVER IS IRREVOCABLE MEANING THAT IT MAY NOT BE MODIFIED EITHER ORALLY OR IN
   WRITING, AND THE WAIVER SHALL APPLY TO ANY SUBSEQUENT AMENDMENTS, RENEWALS,
   SUPPLEMENTS OR MODIFICATIONS TO THIS NOTE, ANY RELATED DOCUMENTS, OR TO ANY
   OTHER DOCUMENTS OR AGREEMENTS RELATING TO THIS TRANSACTION OR ANY RELATED
   TRANSACTION. IN THE EVENT OF LITIGATION, THIS NOTE MAY BE FILED AS A WRITTEN
   CONSENT TO A TRIAL BY THE COURT.

   This Note and any Security Agreement constitute the entire agreement of the
   Maker and Payee with respect to the subject matter hereof and supercedes all
   prior understandings, agreements and representations, express or implied.

   No variation or modification of this Note, or any waiver of any of its
   provisions or conditions, shall be valid unless in wiring and signed by an
   authorized representative of Maker and Payee. Any such waiver, consent,
   modification or change shall be effective only in the specific instance and
   for the specific purpose given.

   Any provision in this Note or any Security Agreement which is in conflict
   with any statute, law or applicable rule shall be deemed omitted, modified or
   altered to conform thereto.

                                     COMBINATORX, INCORPORTED

   /s/ Joseph I Chiapponi            By: /s/ Paul Brannelly
   ------------------------------        ------------------------------------
   (Witness)
      Joseph I Chiapponi             Name: Paul Brannelly
   ------------------------------          ----------------------------------
   (Print name)
   650 Albany St Boston MA 02118     Title: Controller
   ------------------------------           ---------------------------------
   (Address)
                                     Federal Tax ID #: 04-3514451
                                                       ----------------------

                                     Address: 650 Albany St, Boston, MA 02118
                                              -------------------------------<Page>

                                                                Exhibit 10.14

                            NEGATIVE PLEDGE AGREEMENT

            THIS NEGATIVE PLEDGE AGREEMENT is made as of September 7, 2004, by
and between ("BORROWER") and LIGHTHOUSE CAPITAL PARTNERS V, L.P. ("LENDER").

      In connection with the Loan Documents being concurrently executed between
Borrower and Lender, Borrower agrees as follows:

      Except as otherwise permitted in the Loan Documents or pursuant to a
licensing, development or other partnering transaction or other business
relationship related to the use or development of Borrower's intellectual
property (a) that is in the Borrower's ordinary course of business, or (b) that
is not material to the financial condition or results of operations of the
Borrower and in which the Borrower receives adequate consideration, or (c) that
is approved by the Borrower's Board of Directors consistent with the Delaware
General Corporation Law, Borrower shall not sell, transfer, assign, mortgage,
pledge, lease, grant a security interest in, or encumber any of Borrower's
intellectual property, including, without limitation, the following:

  1)  Any and all copyright rights, copyright applications, copyright
      registration and like protection in each work or authorship and derivative
      work thereof, whether published or unpublished and whether or not the same
      also constitutes a trade secret, now or hereafter existing, created,
      acquired or held (collectively, the "COPYRIGHTS");

  2)  Any and all trade secrets, and any and all intellectual property rights in
      computer software and computer software products now or hereafter
      existing, created, acquired or held;

  3)  Any and all design rights which may be available to Borrower now or
      hereafter existing, created, acquired or held;

  4)  All patents, patent applications and like protections, including, without
      limitation, improvements, divisions, continuations, renewals, reissues,
      extensions and continuations-in-part of the same, including, without
      limitation, the patents and patent applications (collectively, the
      "PATENTS");

  5)  Any trademark and servicemark rights, whether registered or not,
      applications to register and registrations of the same and like
      protections, and the entire goodwill of the business of Borrower connected
      with and symbolized by such trademarks (collectively, the "TRADEMARKS");

  6)  All licenses or other rights to use any of the Copyrights, Patents or
      Trademarks and all license fees and royalties arising from such use to the
      extent permitted by such license or rights; and

  7)  All amendments, extensions, renewals and extensions of any of the
      Copyrights, Patents or Trademarks; and

            It shall be an Event of Default under the Loan Documents between
Borrower and Lender if there is a breach of any term of this Negative Pledge
Agreement.

                                        1
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            Capitalized items used herein without definition shall have the same
meanings as set forth in the Loan and Security Agreement of even date herewith.

BORROWER:                               LENDER:

COMBINATORX, INCORPORATED               LIGHTHOUSE CAPITAL PARTNERS V, L.P.

By: /s/ Robert Forrester                BY:     LIGHTHOUSE MANAGEMENT PARTNERS
   --------------------------------             V, L.L.C., its general partner

Name: Robert Forrester
     --------------------------------

Title: CFO                             By: /s/ Thomas Conneely
      -------------------------------      ---------------------------

                                        Name: Thomas Conneely
                                             ------------------------

                                        Title: Vice President
                                              ------------------------

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