Amended & Restated 2004 Incentive Plan



 Exhibit 4.1 

COMBINATORX, INCORPORATED 

AMENDED AND RESTATED 

2004 INCENTIVE PLAN 
  

	1.	DEFINED TERMS 


Exhibit A, which is incorporated by reference, defines the terms used in the Plan and sets forth certain operational
rules related to those terms. 
  

	2.	PURPOSE 

 The Plan has
been established to advance the interests of the Company by providing for the grant to Participants of Stock-based and other incentive Awards. 
  

	3.	ADMINISTRATION 

 The
Administrator has discretionary authority, subject only to the express provisions of the Plan, to interpret the Plan; determine eligibility for and grant Awards; determine, modify or waive the terms and conditions of any Award; prescribe forms,
rules and procedures; and otherwise do all things necessary to carry out the purposes of the Plan. In the case of any Award that is intended to be eligible for the performance-based compensation exception under Section 162(m), the
Administrator will exercise its discretion consistent with qualifying the Award for that exception. Determinations of the Administrator made under the Plan will be conclusive and will bind all parties. 

 

	4.	LIMITS ON AWARDS UNDER THE PLAN 


(a) Number of Shares. Subject to adjustment as provided in Section 7, the maximum number of shares of Stock of the
Company reserved and available for issuance under the Plan shall be (i) 20,000,000 shares of Stock, plus (ii) as of the first day of each of fiscal 2010 through 2015, inclusive, an additional number of shares equal to the least of
(x) 4,000,000 shares of Stock, (y) 4% of the number of then outstanding shares of Stock, and (z) such lesser number as determined by the Administrator. Notwithstanding the preceding sentence, no more than 20,000,000 shares of Stock
may be delivered in satisfaction of ISOs awarded under the Plan. For purposes of this Section 4(a), the shares of Stock underlying any Awards (including any awards granted pursuant to the Prior Plan) that are forfeited, canceled, held back upon
exercise of a Stock Option or settlement of an Award to cover the exercise price or tax withholding, reacquired by the Company prior to vesting, satisfied without the issuance of Stock or otherwise terminated (other than by exercise) shall be added
back to the shares of Stock available for issuance under the Plan. To the extent consistent with the requirements of Section 422 of the Code and regulations thereunder, and with other applicable legal requirements (including applicable stock
exchange or similar requirements), Stock issued under awards of an acquired company that are converted, replaced, or adjusted in connection with the acquisition shall not reduce the number of shares available for Awards under the Plan. 







 (b) Type of Shares. Stock delivered by the Company under the Plan may be
authorized but unissued Stock or previously issued Stock acquired by the Company. No fractional shares of Stock will be delivered under the Plan. 

(c) Additional Limits. The maximum number of shares of Stock for which Stock Options may be granted to any person in
any calendar year and the maximum number of shares of Stock subject to SARs granted to any person in any calendar year will each be 1,500,000. The maximum number of shares of Stock subject to other Awards granted to any person in any calendar year
will be 1,500,000 shares. The maximum amount payable to any person in any year under Cash Awards will be $5,000,000. The foregoing provisions will be construed in a manner consistent with Section 162(m). 

 

	5.	ELIGIBILITY AND PARTICIPATION 


The Administrator will select Participants from among those key Employees and directors of, and consultants and advisors to, the Company
or its Affiliates who, in the opinion of the Administrator, are in a position to make a significant contribution to the success of the Company and its Affiliates. Eligibility for ISOs is limited to employees of the Company or of a “parent
corporation” or “subsidiary corporation” of the Company as those terms are defined in Section 424 of the Code. 
  

	6.	RULES APPLICABLE TO AWARDS 


(a) ALL AWARDS 

(1) Award Provisions. The Administrator will determine the terms of all Awards, subject to the
limitations provided herein. By accepting any Award granted hereunder, the Participant agrees to the terms of the Award and the Plan. Notwithstanding any provision of this Plan to the contrary, awards of an acquired company that are converted,
replaced or adjusted in connection with the acquisition may contain terms and conditions that are inconsistent with the terms and conditions specified herein as determined by the Administrator. 

(2) Term of Plan. No Awards may be made after May 30, 2016, but previously granted Awards may
continue beyond that date in accordance with their terms. 
 (3) Transferability. Neither ISOs
nor, except as the Administrator otherwise expressly provides, other Awards may be transferred other than by will or by the laws of descent and distribution, and during a Participant’s lifetime ISOs (and, except as the Administrator otherwise
expressly provides, other non-transferable Awards requiring exercise) may be exercised only by the Participant. 

(4) Vesting, Etc. The Administrator may determine the time or times at which an Award will vest or
become exercisable and the terms on which an Award requiring exercise will remain exercisable. Without limiting the foregoing, the Administrator may at any time accelerate the vesting or exercisability of an Award, regardless of any adverse or
potentially adverse tax consequences resulting from such acceleration. Unless the Administrator expressly provides otherwise, immediately upon 

 

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the cessation of the Participant’s Employment an Award requiring exercise will cease to be exercisable and will terminate, and all other Awards to the extent not already vested will be
forfeited, except that: 
 (A) subject to (B) and (C) below, all Stock Options and SARs held by
the Participant or the Participant’s permitted transferee, if any, immediately prior to the cessation of the Participant’s Employment, to the extent then exercisable, will remain exercisable for the lesser of (i) a period of three
months or (ii) the period ending on the latest date on which such Stock Option or SAR could have been exercised without regard to this Section 6(a)(4), and will thereupon terminate; 

(B) all Stock Options and SARs held by a Participant or the Participant’s permitted transferee, if any,
immediately prior to the Participant’s death, to the extent then exercisable, will remain exercisable for the lesser of (i) the one year period ending with the first anniversary of the Participant’s death or (ii) the period
ending on the latest date on which such Stock Option or SAR could have been exercised without regard to this Section 6(a)(4), and will thereupon terminate; and 

(C) all Stock Options and SARs held by a Participant or the Participant’s permitted transferee, if any,
immediately prior to the cessation of the Participant’s Employment will immediately terminate upon such cessation if the Administrator in its sole discretion determines that such cessation of Employment has resulted for reasons which cast such
discredit on the Participant as to justify immediate termination of the Award. 
 (5) Taxes.
The Administrator will make such provision for the withholding of taxes as it deems necessary. The Administrator may, but need not, hold back shares of Stock from an Award or permit a Participant to tender previously owned shares of Stock in
satisfaction of tax withholding requirements (but not in excess of the minimum withholding required by law). 

(6) Dividend Equivalents, Etc. The Administrator may provide for the payment of amounts in lieu of cash
dividends or other cash distributions with respect to Stock subject to an Award. Any entitlement to dividend equivalents or similar entitlements shall be established and administered consistent either with exemption from, or compliance with, the
requirements of Section 409A to the extent applicable. 
 (7) Rights Limited. Nothing in
the Plan will be construed as giving any person the right to continued employment or service with the Company or its Affiliates, or any rights as a stockholder except as to shares of Stock actually issued under the Plan. The loss of existing or
potential profit in Awards will not constitute an element of damages in the event of termination of Employment for any reason, even if the termination is in violation of an obligation of the Company or Affiliate to the Participant. 

(8) Certain Performance Awards. This Section 6(a)(8) applies to any Performance Award that is
intended to qualify as performance-based for the purposes of Section 162(m), other than a Stock Option or SAR. In the case of any Performance 

 

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Award to which this Section 6(a)(8) applies, the Plan and such Award will be construed to the maximum extent permitted by law in a manner consistent with qualifying the Award for such
exception. With respect to such Performance Awards, the Administrator will preestablish, in writing, one or more specific Performance Criteria no later than 90 days after the commencement of the period of service to which the performance relates (or
at such earlier time as is required to qualify the Award as performance-based under Section 162(m)). Prior to grant, vesting or payment of the Performance Award, as the case may be, the Administrator will certify whether the applicable
Performance Criteria have been attained and such determination will be final and conclusive. 
 (b) AWARDS REQUIRING
EXERCISE 
 (1) Time And Manner Of Exercise. Unless the Administrator expressly provides
otherwise, an Award requiring exercise by the holder will not be deemed to have been exercised until the Administrator receives a notice of exercise (in form acceptable to the Administrator) signed by the appropriate person and accompanied by
any payment required under the Award. If the Award is exercised by any person other than the Participant, the Administrator may require satisfactory evidence that the person exercising the Award has the right to do so. 

(2) Exercise Price. The Administrator will determine the exercise price (or the base value from which
appreciation is to be measured, in the case of a SAR) of each Award requiring exercise. However, the exercise price or base value, as the case may be, may not be less than the fair market value of the Stock subject to the Award, determined as of the
date of grant. Fair market value shall be determined by the Administrator consistent with the requirements of Section 422, where applicable, and Section 409A. No such Award, once granted, may be repriced other than in accordance with the
applicable Nasdaq stockholder approval requirements. 
 (3) Payment Of Exercise Price. Where
the exercise of an Award is to be accompanied by payment, the Administrator may determine the required or permitted forms of payment, subject to the following: all payments will be by cash or check acceptable to the Administrator, or, if so
permitted by the Administrator and if legally permissible, (i) through the delivery of shares of Stock that have been outstanding for at least six months (unless the Administrator approves a shorter period) and that have a fair market value
equal to the exercise price, (ii) by delivery to the Company of a promissory note of the person exercising the Award, payable on such terms as are specified by the Administrator, (iii) through a broker-assisted exercise program acceptable
to the Administrator, (iv) by other means acceptable to the Administrator, (v) with respect to any Stock Options that are not ISOs, by a “net exercise” arrangement pursuant to which the Company will reduce the number of shares of
Stock issuable upon exercise by the largest whole number of shares with a fair market value that does not exceed the aggregate exercise price, or (vi) by any combination of the foregoing permissible forms of payment. The delivery of shares in
payment of the exercise price under clause (a)(i) above may be accomplished either by actual delivery or by constructive delivery through attestation of ownership, subject to such rules as the Administrator may prescribe. 

 

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 (4) Section 409A Exemption. Except as the
Administrator otherwise determines, no Award requiring exercise shall have deferral features, or shall be administered in a manner, that would cause such Award to fail to qualify for exemption from Section 409A. To the extent that any Award is
determined to constitute “nonqualified deferred compensation” within the meaning of Section 409A (a “409A Award”), the Award shall be subject to such additional rules and requirements as specified by the Administrator from
time to time in order to comply with Section 409A. In this regard, if any amount under a 409A Award is payable upon a “separation from service” (within the meaning of Section 409A) to a grantee who is then considered a
“specified employee” (within the meaning of Section 409A), then no such payment shall be made prior to the date that is the earlier of (i) six months and one day after the grantee’s separation from service, or (ii) the
grantee’s death, but only to the extent such delay is necessary to prevent such payment from being subject to interest, penalties and/or additional tax imposed pursuant to Section 409A. Further, the settlement of any such Award may not be
accelerated except to the extent permitted by Section 409A. 
 (c) AWARDS NOT REQUIRING EXERCISE 

Restricted Stock and Unrestricted Stock, whether delivered outright or under Awards of Stock Units or other Awards that do not require
exercise, may be made in exchange for such lawful consideration, including services, as the Administrator determines. Any Award resulting in a deferral of compensation subject to Section 409A shall be construed to the maximum extent possible,
as determined by the Administrator, consistent with the requirements of Section 409A. 
  

	7.	EFFECT OF CERTAIN TRANSACTIONS 


(a) MERGERS, ETC. 

Except as otherwise provided in an Award, the following provisions shall apply in the event of a Covered Transaction. In the event of a
Covered Transaction in which there is an acquiring or surviving entity, the Administrator may provide for the assumption of some or all outstanding Awards, or for the grant of new awards in substitution therefor, by the acquiror or survivor or an
affiliate of the acquiror or survivor, in each case on such terms and subject to such conditions as the Administrator determines. In the event of a Covered Transaction (whether or not there is an acquiring or surviving entity) where there is no such
assumption or substitution, each Stock Option, SAR and other Award requiring exercise will become fully exercisable, and the delivery of shares of Stock issuable under each outstanding Award of Stock Units (including Restricted Stock Units) will be
accelerated and such shares will be issued, prior to the Covered Transaction, in each case on a basis that gives the holder of the Award a reasonable opportunity, as determined by the Administrator, following exercise of the Award or the issuance of
the shares, as the case may be, to participate as a stockholder in the Covered Transaction, and the Award will terminate upon consummation of the Covered Transaction. Any shares of Stock issued pursuant to the preceding sentence in satisfaction of
an Award may, in the discretion of the Administrator, contain such restrictions, if any, as the Administrator deems appropriate to reflect any performance or other vesting conditions to which the Award was subject. In the case of Restricted Stock,
the Administrator may require that any amounts delivered, exchanged or otherwise paid in respect of such Stock in connection with the Covered Transaction be placed in escrow or otherwise made subject to such restrictions as the Administrator deems
appropriate to carry out the intent of the Plan. 
  

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 (b) CHANGES IN AND DISTRIBUTIONS WITH RESPECT TO THE STOCK 

(1) Basic Adjustment Provisions. In the event of a stock dividend, stock split or combination of shares
(including a reverse stock split), recapitalization or other change in the Company’s capital structure, the Administrator shall make appropriate adjustments to the maximum number of shares specified in Section 4(a) that may be
delivered under the Plan, to the maximum number of shares specified in Section 4(a) that may be issued upon the exercise of ISOs, and to the maximum share limits described in Section 4(c), and shall also make appropriate adjustments
to the number and kind of shares of stock or securities subject to Awards then outstanding or subsequently granted, any exercise prices relating to Awards and any other provision of Awards affected by such change. The Administrator shall also make
equitable or proportionate adjustments in the number of shares subject to outstanding Awards and the exercise price and the terms of outstanding Awards to take into consideration cash dividends paid other than in the ordinary course or any other
extraordinary corporate event. 
 (2) Certain Other Adjustments. The Administrator may also
make adjustments of the type described in Section 7(b)(1) above to take into account distributions to stockholders other than those provided for in Section 7(a) and 7(b)(1), or any other event, if the Administrator determines
that adjustments are appropriate to avoid distortion in the operation of the Plan, having due regard for the qualification of ISOs under Section 422, the requirements of Section 409A, and the performance-based compensation rules of
Section 162(m), where applicable. 
 (3) Continuing Application of Plan Terms. References
in the Plan to shares of Stock will be construed to include any stock or securities resulting from an adjustment pursuant to this Section 7. 
  

	8.	LEGAL CONDITIONS ON DELIVERY OF STOCK 


The Company will not be obligated to deliver any shares of Stock pursuant to the Plan or to remove any restriction from shares of Stock
previously delivered under the Plan until: (i) the Company is satisfied that all legal matters in connection with the issuance and delivery of such shares have been addressed and resolved; (ii) if the outstanding Stock is at the time of
delivery listed on any stock exchange or national market system, the shares to be delivered have been listed or authorized to be listed on such exchange or system upon official notice of issuance; and (iii) all conditions of the Award have been
satisfied or waived. If the sale of Stock has not been registered under the Securities Act of 1933, as amended, the Company may require, as a condition to exercise of the Award, such representations or agreements as counsel for the Company may
consider appropriate to avoid violation of such Act. The Company may require that certificates evidencing Stock issued under the Plan bear an appropriate legend reflecting any restriction on transfer applicable to such Stock, and the Company may
hold the certificates pending lapse of the applicable restrictions. 
  

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	9.	AMENDMENT AND TERMINATION 


The Administrator may at any time or times amend the Plan or any outstanding Award for any purpose which may at the time be permitted by
law, and may at any time terminate the Plan as to any future grants of Awards; provided, that except as otherwise expressly provided in the Plan the Administrator may not, without the Participant’s consent, alter the terms of an Award so
as to affect adversely the Participant’s rights under the Award, unless the Administrator expressly reserved the right to do so at the time of the Award. Amendment to the Plan shall be conditioned upon stockholder approval only to the extent,
if any, such approval is required by law (including the Code and applicable stock exchange requirements), as determined by the Administrator. Notwithstanding any other provision of the Plan to the contrary (including, without limitation,
Section 6(b)(2)), upon approval of the Company’s stockholders, the Administrator may provide for, and the Company may implement, an option exchange offer, pursuant to which certain outstanding Stock Options could, at the election of the
person holding such Stock Option, be tendered to the Company for cancellation in exchange for the issuance of a lesser amount of Stock Options with a lower exercise price. 

 

	10.	OTHER COMPENSATION ARRANGEMENTS 


The existence of the Plan or the grant of any Award will not in any way affect the Company’s right to Award a person bonuses or other
compensation in addition to Awards under the Plan. 
  

	11.	MISCELLANEOUS 


(a) Waiver of Jury Trial. By accepting an Award under the Plan, each Participant waives any right to a trial by jury in
any action, proceeding or counterclaim concerning any rights under the Plan and any Award, or under any amendment, waiver, consent, instrument, document or other agreement delivered or which in the future may be delivered in connection therewith,
and agrees that any such action, proceedings or counterclaim shall be tried before a court and not before a jury. By accepting an Award under the Plan, each Participant certifies that no officer, representative, or attorney of the Company has
represented, expressly or otherwise, that the Company would not, in the event of any action, proceeding or counterclaim, seek to enforce the foregoing waivers. 

(b) Limitation of Liability. Notwithstanding anything to the contrary in the Plan, neither the Company nor the
Administrator, nor any person acting on behalf of the Company or the Administrator, shall be liable to any Participant or to the estate or beneficiary of any Participant by reason of any acceleration of income, or any additional tax, asserted by
reason of the failure of an Award to satisfy the requirements of Section 422 or Section 409A or by reason of Section 4999 of the Code; provided, that nothing in this Section 11(b) shall limit the ability of the
Administrator or the Company to provide by express agreement with a Participant for a gross-up payment or other payment in connection with any such tax or additional tax. 
  


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 (c) Forfeiture of Awards under Sarbanes-Oxley Act. If the Company is required
to prepare an accounting restatement due to the material noncompliance of the Company, as a result of misconduct, with any financial reporting requirement under the securities laws, then any grantee who is one of the individuals subject to automatic
forfeiture under Section 304 of the Sarbanes-Oxley Act of 2002 shall reimburse the Company for the amount of any Award received by such individual under the Plan during the 12-month period following the first public issuance or filing with the
United States Securities and Exchange Commission, as the case may be, of the financial document embodying such financial reporting requirement. 
  

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 EXHIBIT A 

Definition of Terms 

The following terms, when used in the Plan, will have the meanings and be subject to the provisions set forth below: 

“Administrator”: The Compensation Committee, except that the Compensation Committee may delegate (i) to one or
more of its members such of its duties, powers and responsibilities as it may determine; (ii) to one or more officers of the Company the power to grant rights or options to the extent permitted by Section 157(c) of the Delaware
General Corporation Law; (iii) to one or more officers of the Company the authority to allocate other Awards among such persons (other than officers of the Company) eligible to receive Awards under the Plan as such delegated officer or officers
determine consistent with such delegation; provided, that with respect to any delegation described in this clause (iii) the Compensation Committee (or a properly delegated member or members of such Committee) shall have authorized the
issuance of a specified number of shares of Stock under such Awards and shall have specified the consideration, if any, to be paid therefor; and (iv) to such Employees or other persons as it determines such ministerial tasks as it deems
appropriate. In the event of any delegation described in the preceding sentence, the term “Administrator” shall include the person or persons so delegated to the extent of such delegation. 

“Affiliate”: Any corporation or other entity owning, directly or indirectly, 50% or more of the outstanding Stock
of the Company, or in which the Company or any such corporation or other entity owns, directly or indirectly, 50% of the outstanding capital stock (determined by aggregate voting rights) or other voting interests. Notwithstanding the preceding, for
purposes of determining eligibility for the grant of an Stock Option or SAR by reason of service with an Affiliate, the term “Affiliate” shall be limited to persons that stand in a relationship to the Company that would result in the
Company and such person being treated as an employer under Section 414(b) or Section 414(c) of the Code except that “at least 50%” shall be substituted for “at least 80%” under Section 1563(a)(1), (2),
and (3) of the Code and Treas. Reg. Section 1.414(c)-2, all in accordance with the definition of “service recipient” under Section 409A of the Code. 

“Award”: Any or a combination of the following: 

(i) Stock Options. 

(ii) SARs. 

(iii) Restricted Stock. 

(iv) Unrestricted Stock. 

(v) Stock Units, including Restricted Stock Units. 

 

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 (vi) Performance Awards. 

(vii) Cash Awards. 

(viii) Awards (other than Awards described in (i) through (vii) above) that are convertible into or
otherwise based on Stock. 
 “Board”: The Board of Directors of the Company. 

“Cash Award”: An Award denominated in cash. 

“Code”: The U.S. Internal Revenue Code of 1986 as from time to time amended and in effect, or any successor statute
as from time to time in effect. 
 “Compensation Committee”: The Compensation Committee of the Board;
provided, that until a Compensation Committee shall have been appointed, the Board shall discharge the duties and shall exercise the authority of the Compensation Committee hereunder and all references herein to the Compensation Committee
shall be deemed to refer to the Board. 
 “Company”: Combinatorx, Incorporated. 

“Covered Transaction”: Any of (i) a consolidation, merger, or similar transaction or series of related
transactions, including a sale or other disposition of stock, in which the Company is not the surviving corporation or which results in the acquisition of all or substantially all of the Company’s then outstanding common stock by a single
person or entity or by a group of persons and/or entities acting in concert, (ii) a sale or transfer of all or substantially all the Company’s assets, or (iii) a dissolution or liquidation of the Company. Where a Covered Transaction
involves a tender offer that is reasonably expected to be followed by a merger described in clause (i) (as determined by the Administrator), the Covered Transaction shall be deemed to have occurred upon consummation of the tender offer.

 “Effective Date”: The date on which the stockholders of the Company approve the Plan. 

“Employee”: Any person who is employed by the Company or an Affiliate. 

“Employment”: A Participant’s employment or other service relationship with the Company and its Affiliates.
Employment will be deemed to continue, unless the Administrator expressly provides otherwise, so long as the Participant is employed by, or otherwise is providing services in a capacity described in Section 5 to the Company or its Affiliates.
If a Participant’s employment or other service relationship is with an Affiliate and that entity ceases to be an Affiliate, the Participant’s Employment will be deemed to have terminated when the entity ceases to be an Affiliate unless the
Participant transfers Employment to the Company or its remaining Affiliates. 
  

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 “ISO”: A Stock Option intended to be an “incentive stock
option” within the meaning of Section 422 of the Code. Each option granted pursuant to the Plan will be treated as providing by its terms that it is to be a non-incentive option unless, as of the date of grant, it is expressly designated
as an ISO. 
 “Participant”: A person who is granted an Award under the Plan. 

“Performance Award”: An Award subject to Performance Criteria. The Committee in its discretion may grant
Performance Awards that are intended to qualify for the performance-based compensation exception under Section 162(m) and Performance Awards that are not intended so to qualify. 

“Performance Criteria”: Specified criteria, other than the mere continuation of Employment or the mere passage of
time, the satisfaction of which is a condition for the grant, exercisability, vesting or full enjoyment of an Award. For purposes of Awards that are intended to qualify for the performance-based compensation exception under Section 162(m), a
Performance Criterion will mean an objectively determinable measure of performance relating to any or any combination of the following (measured either absolutely or by reference to an index or indices and determined either on a consolidated basis
or, as the context permits, on a divisional, subsidiary, line of business, project or geographical basis or in combinations thereof): sales; revenues; assets; expenses; earnings before or after deduction for all or any portion of interest, taxes,
depreciation, or amortization, whether or not on a continuing operations or an aggregate or per share basis; return on equity, investment, capital or assets; one or more operating ratios; borrowing levels, leverage ratios or credit rating; economic
value created or added; market share; capital expenditures; cash flow; stock price; stockholder return; successful hiring of key individuals; introduction or development of new technologies; product introduction or development, any clinical trial
accomplishments, regulatory or other filings or approvals, other product development milestones; geographic business expansion; cost targets; employee satisfaction; information technology development or acquisition; manufacturing or process
development; resolution of significant litigation; legal compliance or risk reduction; patent application or patent issuances; sales of particular products or services; customer acquisition or retention; acquisitions and divestitures (in whole or in
part); corporate development, including without limitation, joint ventures, collaborations and strategic alliances; spin-offs, split-ups and the like; reorganizations; or recapitalizations, restructurings, financings (issuance of debt or equity) or
refinancings. A Performance Criterion and any targets with respect thereto determined by the Administrator need not be based upon an increase, a positive or improved result or avoidance of loss. To the extent consistent with the requirements for
satisfying the performance-based compensation exception under Section 162(m), to the extent applicable, the Administrator may provide in the case of any Award intended to qualify for such exception that one or more of the Performance Criteria
applicable to such Award will be adjusted in an objectively determinable manner to reflect events (for example, but without limitation, acquisitions or dispositions) occurring during the performance period that affect the applicable Performance
Criterion or Criteria. 
 “Plan”: The Combinatorx, Incorporated 2004 Amended and Restated Incentive Plan
as from time to time amended and in effect. 
  

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 “Prior Plan”: The CombinatoRx, Incorporated 2000 Stock Option Plan as
amended from time to time. 
 “Restricted Stock”: An Award of Stock for so long as the Stock remains
subject to restrictions requiring that it be redelivered or offered for sale to the Company if specified conditions are not satisfied. 

“Restricted Stock Unit”: A Stock Unit that is, or as to which the delivery of Stock or cash in lieu of Stock is,
subject to the satisfaction of specified performance or other vesting conditions. 

“Section 162(m)”: Section 162(m) of the Code. 

“Section 409A”: Section 409A of the Code. 

“SARs”: Rights entitling the holder upon exercise to receive cash or Stock, as the Administrator determines, equal
to a function (determined by the Administrator using such factors as it deems appropriate) of the amount by which the Stock has appreciated in value since the date of the Award. 

“Stock”: Common Stock of the Company, par value $.001 per share. 

“Stock Unit”: An unfunded and unsecured promise, denominated in shares of Stock, to deliver Stock or cash measured
by the value of Stock in the future. 
 “Stock Options”: Options entitling the recipient to acquire shares
of Stock upon payment of the exercise price. 
 “Unrestricted Stock”: An Award of Stock not subject to any
restrictions under the terms of the Award. 
  

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