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                                                                  Exhibit 10.9

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER
THE SECURITIES ACT OF 1933, AS AMENDED, OR ANY STATE SECURITIES LAWS, AND MAY
NOT BE SOLD, PLEDGED, OR OTHERWISE TRANSFERRED WITHOUT AN EFFECTIVE REGISTRATION
THEREOF UNDER SUCH ACT AND LAWS, OR PURSUANT TO RULE 144 AND EXEMPTIONS UNDER
APPLICABLE STATE SECURITIES LAWS, OR, SUBJECT TO SECTION 4.3 HEREOF, AN OPINION
OF COUNSEL REASONABLY SATISFACTORY TO THE CORPORATION AND ITS COUNSEL, THAT SUCH
REGISTRATION IS NOT REQUIRED.

                            WARRANT TO PURCHASE STOCK

Issuer: CombinatoRx, Incorporated, a Delaware corporation
Number of Shares: 315, subject to adjustment           X 50 = 15,750
Class of Stock: Series B Convertible Preferred Stock
Exercise Price: $224.89 per share, subject to adjustment  DIVIDED BY 50 = $4.50
Issue Date: April 25, 2001
Expiration Date: As provided below

     THIS WARRANT CERTIFIES THAT, for the agreed upon value of $1.00 and for
other good and valuable consideration, this Warrant is issued to Silicon Valley
Bank (together with its successors and permitted assigns, "Holder") by
CombinatoRx, Incorporated, a Delaware corporation (the "Company").

     Subject to the terms and conditions hereinafter set forth, the Holder is
entitled upon surrender of this Warrant and the duly executed subscription form
annexed hereto as APPENDIX 1, at the office of the Company, 801 Albany Street,
Suite G02, Boston, Massachusetts 02118, or such other office as the Company
shall notify the Holder of in writing, to purchase from the Company Three
Hundred Fifteen (315) fully paid and non-assessable shares (the "Shares") of the
Company's Series B Convertible Preferred Stock, $.001 par value per share (the
"Class"), at a purchase price per Share of $224.89 (the "Exercise Price"). Until
such time as this Warrant is exercised in full or expires, the Exercise Price
and the number Shares are subject to adjustment from time to time as hereinafter
provided. This Warrant may be exercised in whole or in part at any time and from
time to time until 5:00 PM. Eastern time April 25, 2011 (the "Expiration Date").

     Notwithstanding the foregoing definition of Class, upon and after the
occurrence of an event which results in the automatic or voluntary conversion,
redemption or retirement of all (but not less than all) of the outstanding
shares of such Class, including without limitation the Company's initial
registered underwritten public offering and sale of its securities ("IPO"), then
from and after the date upon which such outstanding shares are so converted,
redeemed or retired. "Class" shall mean the Company's common stock, $.001 par
value per share ("Common Stock"), and this Warrant shall be exercisable for such
number of shares of Common Stock as shall equal the number of shares of Common
Stock into which the Shares would have been converted pursuant to the Company's
Certificate of Incorporation, as amended, including without limitation the
Certificate of Designation, if any, applicable to the same class or series of
preferred stock as the Shares (the "Certificate") had the Shares been issued and
outstanding immediately prior to such conversion, redemption or retirement.

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and the Exercise Price shall be the Common Stock conversion price as determined
pursuant to the Certificate immediately prior to such conversion, redemption or
retirement (all subject to further adjustment as provided herein).

ARTICLE 1. EXERCISE.

           1.1    METHOD OF EXERCISE. Holder may exercise this Warrant by
delivering this Warrant together with a duly executed Notice of Exercise in
substantially the form attached as APPENDIX 1 hereto 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 the aggregate
Exercise Price for the Shares being purchased.

           1.2    CONVERSION RIGHT. In lieu of exercising this Warrant 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 as follows:

                    X = Y (A-B)/A

     where:

                    X = the number of Shares to be issued to the Holder.

                    Y = the number of Shares with respect to which this Warrant
                    is being exercised.

                    A = the Fair Market Value (as determined pursuant to Section
                    1.3 below) of one Share.

                    B = the Exercise Price.

           1.3    FAIR MARKET VALUE.

                  1.3.1  If shares of the Class (or shares of the Company's
stock into which shares of the Class are convertible or exchangeable) are traded
on a nationally recognized securities exchange or over the counter market, the
fair market value of a Share shall be the closing price of a share of the Class
(or the closing price of a share of the Company's stock for which shares of the
Class are convertible or exchangeable) reported for the business day immediately
preceding the date of Holder's Notice of Exercise to the Company.

                  1.3.2  If shares of the Class (or shares of the Company's
stock into which shares of the Class are convertible or exchangeable) are not
traded on a nationally recognized securities exchange or over the counter
market, the Board of Directors of the Company shall determine fair market value
in its reasonable good faith judgment. The foregoing notwithstanding, if Holder
advises the Board of Directors in writing that Holder disagrees with such
determination, then the Company and Holder shall promptly agree upon a reputable
investment banking firm to undertake such valuation. If the valuation of such
investment banking firm is greater than that determined by the Board of
Directors by 10% or more, then all fees and expenses of such investment banking
firm shall be paid by the

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Company. In all other circumstances, such fees and expenses shall be paid by
Holder. The valuation determined by such investment banking firm shall be
conclusive in any event.

           1.4    DELIVERY OF CERTIFICATE AND NEW WARRANT. Promptly after Holder
exercises or converts this Warrant, the Company at its sole expense shall
promptly deliver to Holder (i) certificates for the Shares acquired upon such
exercise, and (ii) if this Warrant has not been fully exercised or converted and
has not expired, a new warrant of like tenor representing the Shares for which
this Warrant is still exercisable.

           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    REPURCHASE ON SALE, MERGER, OR CONSOLIDATION OF THE COMPANY.

                  1.6.1. "ACQUISITION". For the purpose of this Warrant,
"Acquisition" means any sale, assignment, transfer, exclusive license, or other
disposition of all or substantially all of the assets of the Company, or any
acquisition, reorganization, consolidation, or merger of the Company where the
holders of the Company's outstanding voting equity securities immediately prior
to the transaction beneficially own 50% or less of the outstanding voting equity
securities of the surviving or successor entity immediately following the
transaction.

                  1.6.2. ASSUMPTION OF WARRANT. Upon the closing of any
Acquisition the successor or surviving entity shall assume the obligations of
this Warrant, and this Warrant shall be exercisable for the same securities,
cash, and property as would be payable for the Shares issuable upon exercise of
the unexercised portion of this Warrant as if such Shares were outstanding on
the record date for the Acquisition and subsequent closing. The Exercise Price
shall be adjusted accordingly, and the Exercise Price and number and class of
Shares shall continue to be subject to adjustment from time to time in
accordance with the provisions hereof.

                  1.6.3  PURCHASE RIGHT. Notwithstanding the foregoing, upon
the closing of any Acquisition in which the consideration paid to the Company or
stockholders is entirely cash or cash equivalents, at the election of Holder,
the Company shall purchase the unexercised portion of this Warrant for cash for
an amount equal to (a) the fair market value of any consideration that would
have been received by Holder in consideration for the Shares had Holder
exercised the unexercised portion of this Warrant immediately before the record
date for determining the shareholders entitled to participate in the proceeds of
the Acquisition, less (b) the aggregate Exercise Price of the Shares, but in no
event less than zero.

ARTICLE 2. ADJUSTMENTS TO THE SHARES.

           2.1    DIVIDENDS, SPLITS, ETC. If the Company declares or pays a
dividend on the outstanding shares of the Class, payable in Common Stock, other
securities or any type of property, or subdivides the outstanding shares of the
Class into a greater number of shares of the Class, or

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subdivides the shares of the Class in a transaction that increases the amount of
Common Stock into which such shares are convertible, then upon exercise of this
Warrant, for each Share acquired. Holder shall receive, without additional cost
to Holder, the total number and kind of securities or property 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, reorganization 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,
reorganization or other event. The Company or its successor shall promptly issue
to Holder a new warrant of like tenor 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 Exercise 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, reorganizations or other events.

           2.3    ADJUSTMENTS FOR COMBINATIONS, ETC. If the outstanding shares
of the Class are combined or consolidated, by reclassification or otherwise,
into a lesser number of shares, the Exercise Price shall be proportionately
increased and the number of Shares issuable upon exercise or conversion of this
Warrant is exercisable shall be proportionately decreased.

           2.4    NO IMPAIRMENT. The Company shall not, by amendment of the
Certificate or its by-laws 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 of 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.

           2.5    ADJUSTMENTS FOR DILUTIVE ISSUANCES. The number of shares of
Common Stock for which the Shares are convertible shall be adjusted from time to
time in accordance with Section 4 of Article III of the Certificate as if the
Shares were issued and outstanding on and as of the date of any such required
adjustment.

           2.6    FRACTIONAL SHARES. No fractional Shares shall be issuable upon
exercise or conversion of the Warrant and the number of Shares to be issued
shall be rounded down to the nearest whole Share. If a fractional Share interest
arises upon any exercise or conversion of this Warrant, the Company shall
eliminate such fractional Share interest by paying Holder an amount computed by
multiplying such fractional interest by the Fair Market Value (determined in
accordance with Section 1.3 above) of one Share.

           2.7    CERTIFICATE AS TO ADJUSTMENTS. Upon each adjustment of the
Exercise Price, number of class of Shares or number of shares of Common Stock or
other securities for which the Shares are convertible or exchangeable, the
Company at its expense shall promptly compute such

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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 at any time and from time to time, upon written request,
furnish Holder with a certificate setting forth the Exercise Price, number and
class of Shares and conversion ratio in effect upon the date thereof and the
series of adjustments leading to such Exercise Price, number and class of Shares
and conversion ratio.

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 due exercise of
this Warrant, and all Common Stock or other securities, if any, issuable upon
due conversion of the Shares, shall, upon issuance, be duly authorized, validly
issued, fully paid and non-assessable, 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 execution and delivery by the Company of this
Warrant and the performance of all obligations of the Company hereunder,
including the issuance to Holder of the right to acquire the Shares, have been
duly authorized by all necessary corporate action on the part of the Company,
and this Warrant Agreement is not inconsistent with the Certificate and/or the
Company's by-laws, does not contravene any law or governmental rule, regulation
or order applicable to it, does not and will not contravene any provision of, or
constitute a default under, any material indenture, mortgage, contract or other
instrument to which it is a party or by which it is bound, and constitutes a
legal, valid and binding agreement of the Company, enforceable in accordance
with its terms.

                  (c)    The authorized capital stock of the Company consists of
224,213 shares, consisting of 143,000 shares of Common Stock, $.001 par value
per share, and 81,213 shares of preferred stock, $.001 par value per share, of
which 10,068 shares have been designated Series A Convertible Preferred Stock,
and 71,145 shares have been designated Series B Convertible Preferred Stock.
SCHEDULE 3.1(c) sets forth all of the outstanding shares of common stock and
preferred stock and outstanding options, warrants, convertible securities,
convertible debentures, and rights to acquire, subscribe for, and/or purchase
any Common Stock, preferred stock and/or other capital stock of the Company or
any securities or debentures convertible into or exchangeable for Common Stock,
preferred stock and/or other capital stock of the Company.

                  (d)    The Company covenants that it shall at all times cause
to be reserved and kept available out of its authorized and unissued shares such
number of shares of the Class and shares of its Common Stock and other
securities as will be sufficient to permit the exercise in full of this Warrant
and the conversion of the Shares into shares of Common Stock or such other
securities.

                  (e)    On and as of the date hereof, (i) $224.89 is the lowest
price per share for which shares of the Class have been sold or issued by the
Company, and the lowest exercise or conversion price per share for which shares
of the Class may be purchased or acquired upon the exercise or conversion of
outstanding securities exercisable or convertible by their terms for shares of
the Class,

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and (ii) the Common Stock conversion price in effect for shares of the Class as
determined pursuant to the Certificate is $224.89.

           3.2    NOTICE OF CERTAIN EVENTS. If the Company proposes at any time
(a) to declare any dividend or distribution upon any of its capital 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 any of its securities; (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; or (e) offer holders of
registration rights the opportunity to participate in an underwritten public
offering of the Company's securities for cash, then, in connection with each
such event, the Company shall give Holder (1) at least 10 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 securities of the Company shall be entitled to receive such dividend,
distribution or rights); (2) in the case of the matters referred to in (c) and
(d) above at least 10 days prior written notice of the date when the same will
take place (and specifying the date on which the holders of securities of the
Company will be entitled to exchange their securities of the Company for
securities or other property deliverable upon the occurrence of such event); and
(3) in the case of the matter referred to in (e) above, the same notice as is
given to the holders of such registration rights.

           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 (a) promptly
after mailing, copies of all notices or other written communications to the
shareholders of the Company, (b) within one-hundred and twenty (120) days after
the end of each fiscal year of the Company, the annual audited financial
statements of the Company certified by independent public accountants of
recognized standing and (c) such other financial statements required under and
in accordance with any loan documents between Holder and the Company or if there
are no such requirements (or if the subject loan(s) no longer are outstanding),
then within forty-five (45) days after the end of each of the first three
quarters of each fiscal year, the Company's quarterly, unaudited financial
statements.

           3.4    REGISTRATION UNDER SECURITIES ACT OF 1933, AS AMENDED. The
shares of Common Stock issuable upon conversion of the Shares (and the Shares,
at all times when the Class is Common Stock) shall have certain registration
rights as set forth in that certain Registration Rights Agreement of even date
herewith between Holder and the Company (the "Registration Rights Agreement").
The Company represents and warrants to Holder that the Company's execution,
delivery and performance of the Registration Rights Agreement (a) has been duly
authorized by all necessary corporate action of the Company's Board of Directors
and shareholders, (b) will not violate the Certificate or the Company's by-laws,
each as amended, (c) will not violate or cause a breach or default (or an event
which with the passage of time or the giving of notice or both, would constitute
a breach or default) under any agreement, instrument, mortgage, deed of trust or
other arrangement to which the Company is a party or by which it or any of its
assets is subject or bound, and (d) does not require the approval, consent or
waiver of or by any shareholder, registration rights holder or other third party
which approval, consent or waiver has not been obtained as of the date of
issuance of this Warrant.

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ARTICLE 4. MISCELLANEOUS.

           4.1    AUTOMATIC CONVERSION UPON EXPIRATION. In the event that, upon
the Expiration Date, the fair market value of one Share (or other security
issuable upon the exercise hereof) as determined in accordance with Section 1.4
above is greater than the Exercise Price in effect on such date, then this
Warrant shall automatically be deemed on and as of such date to be converted
pursuant to Section 1.2 above as to all Shares (or such other securities) for
which it shall not previously have been exercised or converted, and the Company
shall promptly deliver a certificate representing the Shares (or such other
securities) issued upon such conversion to the Holder.

           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, OR ANY STATE SECURITIES LAWS, AND MAY NOT BE SOLD,
     PLEDGED OR OTHERWISE TRANSFERRED WITHOUT AN EFFECTIVE REGISTRATION
     THEREOF UNDER SUCH ACT AND LAWS, OR PURSUANT TO RULE 144 AND
     EXEMPTIONS UNDER APPLICABLE STATE SECURITIES LAWS, OR, SUBJECT TO
     SECTION 4.3 HEREOF. 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 (and the securities, if any, issued and issuable, upon
conversion of the Shares) 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, as reasonably requested by the Company). The
Company shall not require Holder to provide an opinion of counsel if the
transfer is to Silicon Valley Bancshares (Holder's parent company) or any
other wholly-owned affiliate of Holder or if (a) there is no material
question as to the availability of current information as referenced in
Rule 144(c), (b) Holder represents that it has complied with Rule 144(d)
and (e) in reasonable detail satisfactory to the Company, (c) the selling
broker represents that it has complied with Rule 144(f), and (d) the
Company is provided with a copy of Holder's notice of proposed sale.

           4.4    TRANSFER PROCEDURE. Following its receipt of this executed
Warrant, Silicon Valley bank will transfer same in whole or in part to its
parent corporation Silicon Valley Bancshares, and thereafter Holder and/or
Silicon Valley Bancshares may, subject to Section 4.3 above, transfer all or
part of this Warrant and/or the Shares (or the securities, if any, issued and
issuable upon conversion of the Shares) at any time and from time to time to The
Silicon Valley Bank Foundation or any other transferee 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, that at all times prior to the Company's IPO, Holder
shall not, without the prior written consent of the Company, transfer this
Warrant (or any part hereof), any Shares, or any securities issued or issuable
upon

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conversion of the Shares, to any person who directly competes with the Company,
unless such transfer is in connection with an Acquisition of the Company by any
such person.

           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, or sent via reputable overnight courier service, fee
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, but in all cases, unless instructed in writing otherwise, the
Company shall deliver a copy of all notices to Holder to Silicon Valley
Bank, Treasury Department, 3003 Tasman Drive, HA-200, Santa Clara,
California 95054.

           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    SURVIVAL OF REPRESENTATIONS, WARRANTIES AND AGREEMENTS. All
representations and warranties of the Company contained herein shall survive the
date of this Warrant, the exercise or conversion of this Warrant (or any part
hereof) and/or the termination or expiration of rights hereunder. All agreements
of the Company contained herein shall survive indefinitely until, by their
respective terms, they are no longer operative.

           4.9    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.

                                      "COMPANY"

                                      COMBINATORX, INCORPORATED

                                      By:    /s/ Alexis Borisy
                                         ---------------------------------

                                      Name:  ALEXIS BORISY
                                           -------------------------------
                                             (Print)
                                      Title: President

                                      By:    /s/ Peter B. Finn
                                         ---------------------------------

                                      Name:  Peter B. Finn
                                           -------------------------------
                                             (Print)
                                      Title: Secretary

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                                   APPENDIX 1

                             NOTICE OF EXERCISE

     1.    The undersigned hereby elects to purchase _______ shares of the _____
stock of _______ pursuant to Section 1.1 of the attached Warrant, and tenders
herewith payment of the Exercise Price of such shares in full.

     1.    The undersigned hereby elects to convert the attached Warrant
into Shares in the manner specified in Section 1.2 of the attached Warrant.
This conversion is exercised with respect to _______ of shares of the ________
Stock of _________.

     [Strike paragraph that does not apply.]

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

                   ----------------------------------
                       (Name)

                   ----------------------------------

                   ----------------------------------
                       (Address)

     3.    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.

                                         ------------------------------
                                               (Signature)

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   (Date)<Page>

                                                                 Exhibit 10.10

                          REGISTRATION RIGHTS AGREEMENT

     THIS REGISTRATION RIGHTS AGREEMENT is entered into as of April 25, 2001, by
and between Silicon Valley Bank ("Purchaser") and CombinatoRx, Incorporated, a
Delaware corporation (the "Company").

                                    RECITALS

     A.   Concurrently with the execution of this Agreement, Purchaser is
acquiring from the Company a Warrant to Purchase Stock (the "Warrant") pursuant
to which Purchaser has rights to acquire from the Company the Shares (as defined
in the Warrant), which Shares when issued shall be either shares of the
Company's common stock, $.001 par value per share ("Common Stock") or shares
that are convertible into shares of Common Stock ("Conversion Shares").

     B.   By this Agreement, Purchaser and the Company desire to set forth the
registration rights of the Conversion Shares or the Shares all as provided
herein.

          NOW, THEREFORE, in consideration of the premises and the mutual
promises, covenants and conditions hereinafter set forth, the parties hereto
mutually agree as follows:

     1.   REGISTRATION RIGHTS. The Company covenants and agrees as follows:

          1.1    DEFINITIONS. For purposes of this Section 1:

                 (a)     The term "register," "registered," and "registration"
refer to a registration effected by preparing and filing a registration
statement or similar document in compliance with the Securities Act of 1933, as
amended, and the rules and regulations thereunder (the "Securities Act"), and
the declaration or ordering of effectiveness of such registration statement or
document;

                 (b)     The term "Registrable Securities" means (i) (A) the
Conversion Shares, or (B) Shares, at any time when the Shares are shares of
Common Stock, and (ii) any Common Stock or other Securities of the Company
issued as (or issuable upon the conversion or exercise of any warrant, right or
other security which is issued as) a dividend or other distribution with respect
to, or in exchange for or in replacement of, the Shares or Conversion Shares.

                 (c)     The terms "Holder" or "Holders" means Purchaser and its
qualifying transferees under subsection 1.9 hereof who hold Registrable
Securities.

                 (d)     The term "SEC" means the Securities and Exchange
Commission.

                 (e)     The terms "Form S-l," "Form S-3" etc. shall mean those
forms with such designations as are required by the SEC and any successor or
replacement forms adopted by the SEC.

          1.2    COMPANY REGISTRATION.

                 (a)     REGISTRATION. If at any time or from time to time, the
Company shall determine to register any of its securities, for its own account
or the account of any of its shareholders, other than a registration on Form S-8
relating solely to employee stock option or purchase plans or on Form S-4
relating solely to an SEC Rule 145 transaction, the Company will:

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                         (i)    promptly give to each Holder written notice
thereof (which shall include a list of the jurisdictions in which the Company
intends to attempt to qualify such securities under the applicable blue sky or
other state securities laws); and

                         (ii)   include in such registration (and
qualifications), and in any underwriting involved therein, all the Registrable
Securities specified in a written request or requests, made within 30 days after
receipt of such written notice from the Company, by any Holder or Holders,
except as set forth in subsection 1.2(c) below.

                 (b)     UNDERWRITING. If the registration of which the Company
gives notice is for a registered public offering involving a firm-commitment
underwriting, the Company shall so advise the Holders as a part of the written
notice given pursuant to subsection 1.2(a)(i). In such event the right of any
Holder to registration pursuant to this subsection 1.2 shall be conditioned upon
such Holder's participation in such underwriting and the inclusion of such
Holder's Registrable Securities in the underwriting to the extent provided
herein. All Holders proposing to distribute their securities through such
underwriting shall (together with the Company and the other shareholders
distributing their securities through such underwriting) enter into an
underwriting agreement in customary form (and not inconsistent with the terms
hereof) with the underwriter or underwriters selected for such underwriting by
the Company.

                 (c)     In the case of any registration of Common Stock by the
Company in a firm-commitment underwriting, if the managing underwriters give
written advice to the Company that marketing factors require a limitation on the
number of shares of Common Stock (or other securities convertible into or
exercisable or exchangeable for Common Stock) to be offered and sold by
stockholders of Company in such offering, there shall be included in the
offering: (i) first, all securities proposed by Company to be sold for its
account; and (ii) second, that number of shares of Common Stock, if any,
requested to be included in such registration statement by Holders and by
stockholders of the Company having contractual rights to include shares in such
registration ("Stockholders"), on a pro rata basis based upon the number of
shares of Common Stock each Holder and each such Stockholder beneficially owns.

          1.3    REGISTRATION ON FORM S-3. If at any time (i) the Holder of
Registrable Securities requests in writing that the Company file a registration
statement on Form S-3 or any successor thereto for a public offering of all or
any portion of the shares of Registrable Securities held by the requesting
Holder, (ii) the aggregate price to the public of such offering would reasonably
be expected to exceed $200,000, and (iii) the Company is a registrant entitled
to use Form S-3 or any successor thereto to register such shares, then the
Company shall use its best efforts to register under the Securities Act on
Form S-3 or any successor thereto, for public sale in accordance with the method
of disposition specified in such notice, the number of shares of Registrable
Securities specified in such notice. Whenever the Company is required by this
Section 1.3 to use its best efforts to effect the registration of Registrable
Securities, each of the procedures and requirements of Sections 1.5(d) and 1.8
(as applicable) shall apply to such registration; PROVIDED, HOWEVER, that the
Company shall not be obligated to register Registrable Securities under this
Section 1.3 (x) on more than one occasion in any six-month period, (y) if
Form S-3 is not available for such offering, or (z) if the Company shall furnish
a certificate signed by the chief executive officer stating that in the good
faith judgment of the Company's Board, it would be seriously detrimental to the
Company to effect an S-3 registration at the requested time, in which event the
Company can defer the requested S-3 registration for up to sixty (60) days in
any twelve (12) month period; provided, however, that the Company shall not
utilize this right more than once in any twelve (12) month period.

          1.4    Expenses of Registration. All expenses incurred in connection
with any registration. qualification or compliance pursuant to this Section 1
including without limitation, all registration, filing and qualification fees,
printing expenses, underwriting fees, discounts and commissions, fees and
disbursements of counsel for the Company and expenses of any special audits
incidental to or required by such registration, shall be borne by the Company.
All expenses of any registered offering not otherwise borne by the Company

                                       -2-
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will be borne pro rata among the Holders, any other shareholders of the Company
participating in such offering and the Company.

          1.5   REGISTRATION PROCEDURES. In the case of each registration,
qualification or compliance effected by the Company pursuant to this
Registration Rights Agreement, the Company will keep each Holder participating
therein advised in writing as to the initiation of each registration,
qualification and compliance and as to the completion thereof. At its expense
the Company will:

                 (a)     Prepare and file with the SEC a registration statement
with respect to such Registrable Securities and use its best efforts to cause
such registration statement to become effective, and, upon the request of the
Holders of a majority of the Registrable Securities registered thereunder, keep
such registration statement effective for up to 120 days (the "Effective
Period").

                 (b)     Prepare and file with the SEC such amendments and
supplements to such registration statement and the prospectus used in connection
with such registration statement as may be necessary to comply with the
provisions of the Securities Act with respect to the disposition of all
securities covered by such registration statement.

                 (c)     Furnish to the Holders such numbers of copies of a
prospectus, including a preliminary prospectus, in conformity with the
requirements of the Securities Act, and such other documents as they may
reasonably request in order to facilitate the disposition of Registrable
Securities covered owned by them.

                 (d)     Use its best efforts to register and qualify the
securities covered by such registration statement under such other securities or
Blue Sky laws of such jurisdictions as shall be reasonably requested by the
Holders, provided that the Company shall not be required in connection therewith
or as a condition thereto to qualify to do business or to file a general consent
to service of process in any states or jurisdictions.

                 (e)     In the event of any underwritten public offering, enter
into and perform its obligations under an underwriting agreement, in usual and
customary form, with the managing underwriter of such offering. Each Holder
participating in such underwriting shall also enter into and perform its
obligations under such an agreement provided that all other shareholders of the
Company participating in such offering do the same.

                 (f)     Notify each Holder of Registrable Securities covered by
such registration statement at any time when a prospectus relating thereto is
required to be delivered under the Securities Act or the happening of any event
as a result of which the prospectus included in such registration statement, as
then in effect, includes an untrue statement of a material fact or omits to
state a material fact required to be stated therein or necessary to make the
statements therein not misleading in the light of the circumstances then
existing.

          1.6    INDEMNIFICATION.

                 (a)     The Company will indemnify each Holder of Registrable
Securities and each of its officers, directors and partners, and each person
controlling such Holder within the meaning of Section 15 of the Securities Act
("controlling person"), and each underwriter, if any, and each controlling
person of such underwriter, with respect to which registration, qualification or
compliance of Registrable Securities has been effected pursuant to this
Registration Rights Agreement, against all claims, losses, expenses, damages and
liabilities (or actions in respect thereto) arising out of or based on any
untrue statement (or alleged untrue statement) of a material fact contained in
any prospectus, offering circular or other document including any related
registration statement, notification or the like) incident to any such
registration,

                                       -3-
<Page>

qualification or compliance, or based on any omission (or alleged omission) to
state therein a material fact required to be stated therein or necessary to make
the statement therein not misleading, or any violation or alleged violation by
the Company of the Securities Act, the Securities Exchange Act of 1934, as
amended, and the rules and regulations thereunder ("Exchange Act") or any state
securities law applicable to the Company or any rule or regulation promulgated
under any such state law and relating to action or inaction required of the
Company in connection with any such registration, qualification or compliance,
and will reimburse each such Holder, each of its officers, directors and
partners, and each person controlling such Holder, each such underwriter and
each person who controls any such underwriter, within a reasonable amount of
time after incurred for any reasonable legal and any other expenses incurred in
connection with, investigating, defending or settling any such claim, loss,
damage, liability or action; PROVIDED, HOWEVER, that the indemnity agreement
contained in this subsection 1.6(a) shall not apply to amounts paid in
settlement of any such claim, loss, damage, liability, or action if such
settlement is effected without the consent of the Company (which consent shall
not be unreasonably withheld or delayed); AND PROVIDED FURTHER, that the Company
will not be liable in any such case to the extent that any such claim, loss,
damage or liability arises out of or is based on any untrue statement or
omission to state a material fact required to be stated or necessary to make a
statement not misleading made in reliance upon and conformity with written
information furnished to the Company by an instrument duly executed by such
Holder specifically for use therein.

                 (b)     Each Holder will, if Registrable Securities held by or
issuable to such Holder are included in the securities as to which such
registration, qualification or compliance is being effected, indemnify the
Company, each of its directors, officers and controlling persons, each
underwriter, if any, of the Company's securities covered by such a registration
statement, and each controlling person of such underwriter, and each other
Holder and Stockholder, each of their officers, directors, partners and
controlling persons, against all claims, losses, expenses, damages and
liabilities (or actions in respect thereof) arising out of or based on any
untrue statement (or alleged untrue statement) of a material fact contained in
any such registration statement, prospectus, offering circular or other
document, or any omission (or alleged omission) to state therein a material fact
required to be stated therein or necessary to make the statements therein not
misleading or any violation by the Holder, its directors, officers, and/or
controlling persons of the Securities Act, the Exchange Act, or any applicable
state securities law or rule or regulation promulgated thereunder, and will
reimburse the Company, such Stockholders, such Holders, such directors,
officers, partners, persons or underwriters for any reasonable legal or any
other expenses incurred in connection with investigating, defending or settling
any such claim, loss, damage, liability or action, in each case to the extent,
but only to the extent, that such untrue statement (or alleged untrue statement)
or omission (or alleged omission) is made in such registration statement,
prospectus, offering circular or other document in reliance upon and in
conformity with written information furnished to the Company by an instrument
duly executed by such Holder specifically for use therein; PROVIDED, HOWEVER,
that the indemnity agreement contained in this subsection 1.6(b) shall not apply
to amounts paid in settlement of any such claim, loss, damage, liability or
action if such settlement is effected without the consent of the Holder, (which
consent shall not be unreasonably withheld or delayed); AND PROVIDED FURTHER,
that the total amount for which any Holder shall be liable under this subsection
1.6(b) shall not in any event exceed the aggregate proceeds received by such
Holder from the sale of Registrable Securities held by such Holder in such
registration.

                 (c)     Each party entitled to indemnification under this
subsection 1.6 (the "Indemnified Party") shall give notice to the party required
to provide indemnification (the "Indemnifying Party") promptly after such
Indemnified Party has actual knowledge of any claim as to which indemnity may be
sought, and shall permit the Indemnifying Party to assume the defense of any
such claim or any litigation, resulting therefrom; provided that counsel for the
Indemnifying Party, who shall conduct the defense of such claim or litigation,
shall be approved by the Indemnified Party (whose approval shall not be
unreasonably withheld), and the Indemnified Party may participate in such
defense at such party's expense; and provided further, that the failure of any
Indemnified Party to give notice as provided herein shall not relieve the
Indemnifying Party of its obligations hereunder, unless such failure resulted in
prejudice to the Indemnifying Party; and provided further, that an Indemnified
Party (together with all other Indemnified Parties which may

                                       -4-
<Page>

be represented without conflict by one counsel) shall have the right to retain
one separate counsel, with the fees and expenses to be paid by the Indemnifying
Party, if representation of such Indemnified Party by the counsel retained by
the Indemnifying Party would be inappropriate due to actual or potential
differing interests between such Indemnified Party and any other party
represented by such counsel in such proceeding. No Indemnifying Party, in the
defense of any such claim or litigation, shall, except with the consent of each
Indemnified Party, consent to entry of any judgment or enter into any settlement
which does not include as an unconditional term thereof the giving by the
claimant or plaintiff to such Indemnified Party of a release from all liability
in respect to such claim or litigation.

          1.7    INFORMATION BY HOLDER. Any Holder or Holders of Registrable
Securities included in any registration shall promptly furnish to the Company
such information regarding such Holder or Holders and the distribution proposed
by such Holder or Holders as the Company may request in writing and as shall be
required in connection with any registration, qualification or compliance
referred to herein.

          1.8    RULE 144 REPORTING AND FORM S-3. With a view to making
available to Holders the benefits of certain rules and regulations of the SEC
which may permit the sale of the Registrable Securities to the public without
registration or pursuant to a registration on Form S-3, the Company agrees at
all times to:

                 (a)     make and keep public information available, as those
terms are understood and defined in SEC Rule 144, after 90 days after the
effective date of the first registration filed by the Company for an offering of
its securities to the general public;

                 (b)     take such action, including the voluntary registration
of its Common Stock under Section 12 of the Exchange Act, as is necessary to
enable the Holders to utilize Form S-3 for the sale of their Registrable
Securities, such action to be taken as soon as practicable after the end of the
fiscal year in which the first registration statement filed by the Company for
the offering of its securities to the general public is declared effective;

                 (c)     file with the SEC in a timely manner all reports and
other documents required of the Company under the Securities Act and the
Exchange Act (at any time after it has become subject to such reporting
requirements); and

                 (d)     so long as a Holder owns any Registrable Securities, to
furnish to such Holder forthwith upon request a written statement by the Company
as to its compliance with the reporting requirements of said Rule 144 (at any
time after 90 days after the effective date of the first registration statement
filed by the Company for an offering of its securities to the general public),
and of the Securities Act and the Exchange Act (at any time after it has become
subject to such reporting requirements), or that it qualifies as a registrant
whose securities may be resold pursuant to S-3 (at any time after it so
qualifies), a copy of the most recent annual or quarterly report of the Company,
and such other reports and documents so filed by the Company as the Holder may
reasonably request in complying with any rule or regulation of the SEC allowing
the Holder to sell any such securities without registration or pursuant to such
form.

          1.9    TRANSFER OF REGISTRATION RIGHTS. Holders' rights to cause the
Company to register their securities and keep information available, granted to
them by the Company under subsections 1.2, 1.3 and 1.8 may be assigned to a
transferee or assignee of a Holder's Registrable Securities not sold to the
public, provided, that the Company is given written notice by such Holder at the
time of or within a reasonable time after said transfer, stating the name and
address of said transferee or assignee and identifying the securities with
respect to which such registration rights are being assigned.

          1.10   MARKET STAND-OFF AGREEMENT. Each Holder hereby agrees that,
during the period of duration specified by the Company and an underwriter of
Common Stock or other securities of the

                                       -5-
<Page>

Company, following the effective date of a registration statement of the Company
filed under the Securities Act, it shall not, to the extent requested by the
Company and such underwriter, directly or indirectly, sell, offer to sell,
contract to sell, grant any option to purchase or otherwise transfer or dispose
of (other than to donees who agree to be similarly bound) any securities of the
Company held by it at any time during such period except Common Stock included
in such registration; provided, however, that:

                 (a)     such restriction shall be applicable only to the first
such registration statement of the Company which covers Common Stock (or other
securities) to be sold on its behalf to the public in an underwritten offering;

                 (b)     such market stand-off time period shall not exceed 180
days;

                 (c)     all officers and directors of the Company and all other
holders of at least 1% of the shares of Common Stock outstanding immediately
prior to such registration enter into similar agreements; and

                 (d)     such market stand-off agreement shall be terminated and
be of no further, force and effect if any Holder, Stockholder, or any officer or
director of the Company or any such 1% holder bound by a similar agreement is
released or otherwise no longer bound by the provisions hereof or thereof and
the Company shall upon request of a Holder certify to such Holder whether or not
it has granted any such release.

     In order to enforce the foregoing covenant, the Company may impose stop
transfer instructions with respect to the Registrable Securities of each Holder
and Stockholder (and the shares of securities of every other person subject to
the foregoing restriction) until the end of such period.

     Notwithstanding the foregoing, the obligations described in this
Section 1.10 shall not apply to a registration relating solely to employee
benefit plans on Form S-l or Form S-8 or similar forms which may be promulgated
in the future, or a registration relating solely to a Commission Rule 145
transaction on Form S-14 or form S-15 or similar forms which may be promulgated
in the future.

          1.11   TERMINATION OF REGISTRATION RIGHTS. No Holder shall be entitled
to exercise any right provided for in this Section 1 after seven (7) years
following the consummation of the sale of securities pursuant to a registration
statement filed by the Company under the Act in connection with the initial firm
commitment underwritten offering of its securities to the general public.

     2.   GENERAL.

          2.1    WAIVERS AND AMENDMENTS. With the written consent of the record
or beneficial holders of at least 50.1% of the Registrable Securities, the
obligations of the Company and the rights of the Holders of the Registrable
Securities under this agreement may be waived (either generally or in a
particular instance, either retroactively or prospectively, and either for a
specified period of time or indefinitely), and with the same consent the
Company, when authorized by resolution of its Board of Directors, may enter into
a supplementary agreement for the purpose of adding any provisions to or
changing in any manner or eliminating any of the provisions of this Agreement;
provided, however, that no such modification, amendment or waiver shall reduce
the aforesaid percentage of Registrable Securities without the consent of all
of the Holders of the Registrable Securities. Upon the effectuation of each such
waiver, consent, agreement of amendment or modification, the Company shall
promptly give written notice thereof to the record holders of the Registrable
Securities who have, not previously consented thereto in writing. This Agreement
or any provision hereof may be changed, waived, discharged or terminated only by
a statement in writing signed by the party against which enforcement of the
change, waiver, discharge or termination is. sought, except to the extent
provided in this subsection 2.1.

                                       -6-
<Page>

          2.2    GOVERNING LAW. This Agreement shall be governed in all respects
by the laws of Commonwealth of Massachusetts as such laws are applied to
agreements between Massachusetts residents entered into and to be performed
entirely within Massachusetts.

          2.3    SUCCESSORS AND ASSIGNS. Except as otherwise expressly provided
herein, the provisions hereof shall inure to the benefit of, and be
binding upon, the successors, assigns, heirs, executors and administrators of
the parties hereto.

          2.4    ENTIRE AGREEMENT. Except as set forth below, this Agreement and
the other documents delivered pursuant hereto constitute the full and entire
understanding and agreement between the parties with regard to the subjects
hereof and thereof.

          2.5    NOTICES, ETC. All notices and other communications required or
permitted hereunder shall be in writing and shall be mailed by first class mail,
postage prepaid, certified or registered mail, return receipt requested, or
reputable overnight courier, addressed (a) if to Holder, at such Holder's
address(es) as set forth below, or at such other address(es) as such Holder
shall have furnished to the Company in writing, or(b) if to the Company, at the
Company's address set forth below, or at such other address as the Company shall
have furnished to the Holder in writing.

          2.6    SEVERABILITY. In case any provision of this Agreement shall be
invalid, illegal, or unenforceable, the validity, legality and enforceability
of the remaining provisions of this Agreement or any provision of the other
Agreement s shall not in any way be affected or impaired thereby.

          2.7.   TITLES AND SUBTITLES. The titles of the sections and
subsections of this Agreement are for convenience of reference only and are not
to be considered in construing this Agreement.

          2.8    COUNTERPARTS. This Agreement may be executed in any number of
counterparts, each of which shall be an original, but all of which together
shall constitute one instrument.

PURCHASERS                                      COMPANY

SILICON VALLEY BANK                             COMBINATORX, INCORPORATED.

By: /s/ Laura M. Scott                          By: /s/ Alexis Borisy
   ----------------------------                    ----------------------------
Name: Laura M. Scott                            Name: Alexis Borisy
     --------------------------                      --------------------------
Title: Vice President                           Title: President
      -------------------------                       -------------------------
Address:                                        Address:
        -----------------------
        -----------------------

copy to:  Silicon Valley Bank
          Treasury Department
          3003 Tasman Drive, HA-200
          Santa Clara, CA 95054

                                       -7-

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