Nonqualified Deferred Compensation Plan, effective December 1, 2007.



 Exhibit 4.1 
 COMBINATORX, INCORPORATED 
 NONQUALIFIED DEFERRED COMPENSATION PLAN 
 This document is intended to comply with Internal Revenue Code Section 409A and regulations promulgated thereunder and shall be administered and construed
accordingly. 







 COMBINATORX NONQUALIFIED DEFERRED COMPENSATION PLAN 
 Table of Contents 
  

					
	 	  	 	  	Page
	
	Article 1 - Definitions
			
	 1.1
	  	Account.	  	1
	 1.2
	  	Administrator.	  	1
	 1.3
	  	Board.	  	1
	 1.4
	  	Bonus.	  	1
	 1.5
	  	Change-in-Control.	  	1
	 1.6
	  	Code.	  	2
	 1.7
	  	Compensation.	  	2
	 1.8
	  	Deferrals.	  	2
	 1.9
	  	Deferral Election.	  	2
	 1.10
	  	Disability.	  	2
	 1.11
	  	Effective Date.	  	2
	 1.12
	  	Eligible Employee.	  	3
	 1.13
	  	Employee.	  	3
	 1.14
	  	Employer.	  	3
	 1.15
	  	Employer Discretionary Contribution.	  	3
	 1.16
	  	ERISA.	  	3
	 1.17
	  	Investment Fund.	  	3
	 1.18
	  	Matching Contribution.	  	3
	 1.19
	  	Participant.	  	3
	 1.20
	  	Plan Year.	  	3
	 1.21
	  	Retirement.	  	3
	 1.22
	  	Salary.	  	3
	 1.23
	  	Separation from Service.	  	4
	 1.24
	  	Service Recipient.	  	4
	 1.25
	  	Specified Employee.	  	4
	 1.26
	  	Trust.	  	4
	 1.27
	  	Trustee.	  	4
	 1.28
	  	Years of Service.	  	4
	
	Article 2 - Participation
			
	 2.1
	  	Commencement of Participation.	  	5
	 2.2
	  	Loss of Eligible Employee Status.	  	5
	
	Article 3 - Contributions
			
	 3.1
	  	Deferral Elections - General.	  	5
	 3.2
	  	Time of Election.	  	5
	 3.3
	  	Distribution Elections.	  	6
	 3.4
	  	Additional Requirements.	  	6









					
	 3.5
	  	Matching Contribution.	  	6
	 3.6
	  	Employer Discretionary Contributions.	  	7
	 3.7
	  	Crediting of Contributions.	  	7
	
	Article 4 - Vesting
			
	 4.1
	  	Vesting of Deferrals.	  	7
	 4.2
	  	Vesting of Matching Contributions.	  	7
	 4.3
	  	Vesting of Employer Discretionary Contributions.	  	7
	 4.4
	  	Vesting in Event of Retirement, Disability, Death or Change-in-Control.	  	8
	 4.5
	  	Amounts Not Vested.	  	8
	 4.6
	  	Forfeitures.	  	8
	
	Article 5 - Accounts
			
	 5.1
	  	Accounts.	  	8
	 5.2
	  	Investments, Gains and Losses.	  	9
	
	Article 6 - Distributions
			
	 6.1
	  	Distribution Election.	  	9
	 6.2
	  	Distributions Upon an In-Service Account Triggering Date.	  	9
	 6.3
	  	Distributions Upon Retirement.	  	10
	 6.4
	  	Substantially Equal Annual Installments.	  	10
	 6.5
	  	Distributions due to other Separation from Service.	  	10
	 6.6
	  	Changes to Distribution Elections.	  	10
	 6.7
	  	Cash-Out Provision.	  	11
	 6.8
	  	Unforeseeable Emergency.	  	11
	 6.9
	  	Distributions to Specified Employee.	  	11
	 6.10
	  	Exception to Separation from Service	  	11
	 6.11
	  	Minimum Distribution.	  	12
	 6.12
	  	Separation from Service for Cause.	  	12
	 6.13
	  	Domestic Relations Orders	  	12
	 6.14
	  	Distributions Upon a Change-in-Control.	  	12
	
	Article 7 - Beneficiaries
			
	 7.1
	  	Beneficiaries.	  	12
	 7.2
	  	Lost Beneficiary.	  	13
	
	Article 8 - Funding
			
	 8.1
	  	Unfunded Arrangement.	  	13
	 8.2
	  	Deposits in Trust.	  	13
	 8.3
	  	Withholding of Employee Contributions.	  	13









					
	
	Article 9 - Claims Administration
			
	9.1	  	 General.
	  	14
	9.2	  	Claims Procedure.	  	14
	9.3	  	Right of Appeal.	  	14
	9.4	  	Review of Appeal.	  	15
	9.5	  	Designation.	  	15
	
	Article 10 - General Provisions
			
	10.1	  	Administrator.	  	15
	10.2	  	No Assignment.	  	16
	10.3	  	No Employment Rights.	  	16
	10.4	  	Incompetence.	  	16
	10.5	  	Identity.	  	16
	10.6	  	Other Benefits.	  	16
	10.7	  	Expenses.	  	17
	10.8	  	Insolvency.	  	17
	10.9	  	Amendment or Modification.	  	17
	10.10	  	Plan Suspension.	  	17
	10.11	  	Plan Termination.	  	17
	10.12	  	Plan Termination due to a Change-in-Control.	  	17
	10.13	  	Construction.	  	18
	10.14	  	Governing Law.	  	18
	10.15	  	Severability.	  	18
	10.16	  	Headings.	  	18
	10.17	  	Terms.	  	18








 COMBINATORX, INCORPORATED 
 NONQUALIFIED DEFERRED COMPENSATION PLAN 
 CombinatoRx, Incorporated, a Delaware
corporation, and its affiliates and subsidiaries (the “Employer”), hereby adopts this CombinatoRx Nonqualified Deferred Compensation Plan (the “Plan”) for the benefit of a select group of management or highly compensated
employees. This Plan is an unfunded arrangement and is intended to be exempt from the participation, vesting, funding, and fiduciary requirements set forth in Title I of ERISA. The Plan is intended to comply with Section 409A of the Code and
shall be administered and construed accordingly. This Plan is effective as of December 1, 2007. 
 Article 1 - Definitions

  

	1.1	Account. 

 The bookkeeping account established for
each Participant as provided in Section 5.1 hereof. 
  

	1.2	Administrator. 

 An administrative committee
appointed by the Board. The Plan Administrator shall serve as the agent for the Employer with respect to the Trust. 
  

	1.3	Board. 

 The Board of Directors of the Employer.

  

	1.4	Bonus. 

 Compensation which is designated as such by
the Employer and which relates to services performed during an incentive period by an Eligible Employee in addition to his or her Salary, including any pretax elective deferrals from said Bonus to any Employer sponsored plan that includes amounts
deferred under a Deferral Election or any elective deferral as defined in Code Section 402(g)(3) or any amount contributed or deferred at the election of the Eligible Employee in accordance with Code Section 125 or 132(f)(4). 

 

	1.5	Change-in-Control. 

 Provided that such definition
shall be interpreted in a manner that is consistent with Code Section 409A and regulations thereunder, a “Change-in-Control” of the Employer (which, for purpose of this Section 1.5 shall mean CombinatoRx, Incorporated but not any
of its affiliates or subsidiaries) shall mean the first to occur of any of the following: 
 (a) the date that any one person or persons
acting as a group acquires ownership of Employer stock constituting more than fifty percent (50%) of the total fair market value or total voting power of the Employer; 
 (b) the date that any one person or persons acting as a group acquires (or has acquired during the 12-month period ending on the date of the most recent
acquisition by such 

  

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person or persons) ownership of the stock of the Employer possessing thirty percent (30%) or more of the total voting power of the stock of the
Employer; 
 (c) the date that any one person or persons acting as a group acquires (or has acquired during the 12-month period ending on the
date of the most recent acquisition by such person or persons) assets from the Employer that have a total gross fair market value equal to or more than forty percent (40%) of the total gross fair market value of all of the assets of the
Employer immediately prior to such acquisition; or 
 (d) the date that a majority of members of the Employer’s Board is replaced during
any 12-month period by directors whose appointment or election is not endorsed by a majority of the members of the Board prior to the date of the appointment or elections. 
  

	1.6	Code. 

 The Internal Revenue Code of 1986, as
amended. 
  

	1.7	Compensation. 

 The Participant’s earned
income, including Salary, Bonus, and other remuneration from the Employer as may be included by the Administrator from time to time, but excluding the following: (i) commission income; (ii) welfare benefits, fringe benefits and any other
noncash remuneration; (iii) amounts realized from the sale, exchange or other disposition of stock acquired under a stock option, a stock grant or any other similar arrangement; and (iv) moving expenses. 
  

	1.8	Deferrals. 

 The portion of Compensation that a
Participant elects to defer in accordance with Section 3.1 hereof. 
  

	1.9	Deferral Election. 

 The separate agreement,
submitted to the Administrator, by which an Eligible Employee agrees to participate in the Plan and make Deferrals thereto. 
  

	1.10	Disability. 

 A Participant shall be considered
disabled if: (i) the Participant is unable to engage in any substantial gainful activity by reason of any medically determinable physical or mental impairment which can be expected to result in death or can be expected to last for a continuous
period of not less than 12 months; (ii) the Participant is, by reason of any medically determinable physical or mental impairment which can be expected to result in death or can be expected to last for a continuous period of not less than 12
months, receiving income replacement benefits for a period of not less than 3 months under an accident and health plan covering employees of the Participant’s Employer; or (iii) determined to be totally disabled by the Social Security
Administration. 
  

	1.11	Effective Date. 

 December 1, 2007. 

 

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	1.12	Eligible Employee. 

 An Employee shall be considered
an Eligible Employee if such Employee is a member of a select group of management or highly compensated employees and is designated as an Eligible Employee by the Administrator. The designation of an Employee as an Eligible Employee in any year
shall not confer upon such Employee any right to be designated as an Eligible Employee in any future Plan Year. 
  

	1.13	Employee. 

 Any person employed by the Employer.

  

	1.14	Employer. 

 CombinatoRx, Incorporated and its
subsidiaries and affiliates. 
  

	1.15	Employer Discretionary Contribution. 

 A
discretionary contribution made by the Employer that is credited to one or more Participant’s Accounts in accordance with the terms of Section 3.6 hereof. 
  

	1.16	ERISA. 

 The Employee Retirement Income Security Act
of 1974, as amended. 
  

	1.17	Investment Fund. 

 Each investment(s) which serves
as a means to measure value, increases or decreases with respect to a Participant’s Accounts. 
  

	1.18	Matching Contribution. 

 A discretionary
contribution made by the Employer that is credited to one or more Participant’s Accounts in accordance with the terms of Section 3.5 hereof. 
  

	1.19	Participant. 

 An Eligible Employee who is a
Participant as provided in Article 2. 
  

	1.20	Plan Year. 

 For the initial Plan Year, Effective
Date through December 31, 2007. For each year thereafter, January 1 through December 31. 
  

	1.21	Retirement. 

 Retirement means either (i) a
Participant has reached age sixty-five (65) and has a Separation from Service, or (ii) a Participant has reached age fifty-five (55) and has five (5) Years of Service and has a Separation from Service. 
  

	1.22	Salary. 

 An Eligible Employee’s base salary
earned during a Plan Year, including any pretax elective deferrals from said Salary to any Employer sponsored plan that includes amounts deferred under a Deferral Election or any elective deferral as defined in Code Section 402(g)(3) 

  

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or any amount contributed or deferred at the election of the Eligible Employee in accordance with Code Section 125 or 132(f)(4). 
  

	1.23	Separation from Service. 

 As provided by
regulations promulgated under Code Section 409A, a Participant shall incur a Separation from Service with the Service Recipient due to death, retirement or other termination of employment with the Service Recipient unless the employment
relationship is treated as continuing intact while the individual is on military leave, sick leave, or other bona fide leave of absence if the period of such leave does not to exceed six months, or if longer, so long as the individual retains a
right to reemployment with the Service Recipient under an applicable statute or by contract. 
  

	1.24	Service Recipient. 

 As provided by regulations
promulgated under Code Section 409A, Service Recipient shall mean the Employer or person for whom the services are performed and with respect to whom the legally binding right to compensation arises, and all persons with whom such person would
be considered a single employer under Code Section 414(b) (employees of controlled group of corporations), and all persons with whom such person would be considered a single employer under Code Section 414(c) (employees of partnerships,
proprietorships, etc., under common control). 
  

	1.25	Specified Employee. 

 Specified Employee shall mean
a participant who is considered a key employee on the Identification Date, as defined in Code Section 416(i) without regard to section 416(i)(5) and such other requirements imposed under Code Section 409A(a)(2)(B)(i) and regulations
thereunder for the period beginning April 1 of the year subsequent to the Identification Date and ending March 31 of the following year. The Identification Date for this Plan is December 31 of each year. Notwithstanding anything to
the contrary, a Participant is not a Specified Employee unless any stock of the Service Recipient is publicly traded on an established securities market or otherwise. 
  

	1.26	Trust. 

 The agreement between the Employer and the
Trustee under which the assets of the Plan are held, administered and managed, which shall be consistent with the terms of Rev. Proc. 92-64. 
  

	1.27	Trustee. 

 State Street Bank and Trust, or such
other successor that shall become trustee pursuant to the terms of the Plan. 
  

	1.28	Years of Service. 

 A Participant’s “Years
of Service” shall be measured by employment during a twelve (12) month period commencing with the Participant’s date of hire and anniversaries thereof. 
  

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 Article 2 - Participation 
  

	2.1	Commencement of Participation. 

 Each Eligible
Employee shall become a Participant at the earlier of the date on which his or her Deferral Election first becomes effective or the date on which an Employer Discretionary Contribution is first credited to his or her Account. 
  

	2.2	Loss of Eligible Employee Status. 

 A Participant
who is no longer an Eligible Employee shall not be permitted to submit a Deferral Election and all Deferrals for such Participant shall cease as of the end of the Plan Year in which such Participant is determined to no longer be an Eligible
Employee. Amounts credited to the Account of a Participant who is no longer an Eligible Employee shall continue to be held pursuant to the terms of the Plan and shall be distributed as provided in Article 6. 
 Article 3 - Contributions 
  

	3.1	Deferral Elections - General. 

 A Participant’s
Deferral Election for a Plan Year is irrevocable for that applicable Plan Year; provided, however that a cessation of Deferrals shall occur if required by the terms of the Employer’s qualified 401(k) plan in order for the Participant to obtain
a hardship withdrawal from the 401(k) plan, or if required under Section 6.8 (Unforeseeable Emergency) of this Plan. Such amounts deferred under the Plan shall not be made available to such Participant, except as provided in Article 6, and
shall reduce such Participant’s Compensation from the Employer in accordance with the provisions of the applicable Deferral Election; provided, however, that all such amounts shall be subject to the rights of the general creditors of the
Employer as provided in Article 8. The Deferral Election, in addition to the requirements set forth below, must designate: (i) the amount or percentage of Compensation to be deferred, (ii) the time of the distribution, and (iii) the
form of the distribution. 
  

	3.2	Time of Election. 

 A Deferral Election shall be
void if it is not made in a timely manner as follows: 
 (a) A Deferral Election with respect to any Compensation must be submitted to the
Administrator before the beginning of the calendar year during which the amount to be deferred will be earned. As of December 31 of each calendar year, said Deferral Election is irrevocable for the calendar year. 
 (b) Notwithstanding the foregoing and in the discretion of the Employer, in a year in which an Employee is first eligible to participate, and provided
that such Employee is not eligible to participate in any other similar account balance arrangement subject to Code Section 409A which would be aggregated with the Plan under the plan aggregation rules promulgated under Code Section 409A,
such Deferral Election shall be submitted within thirty (30) days after the date on which an Employee is first eligible to participate, and such Deferral Election shall apply to Compensation to be earned during the remainder of the calendar
year after such election is made. 
  

 5 









	3.3	Distribution Elections. 

 At the time a Participant
makes a Deferral Election, he or she must also elect the time and form of the distribution by establishing one or more In-Service Account(s) or Retirement Account(s) as provided in Sections 5.1 and 6.1. If the Participant fails to properly designate
the time and form of a distribution, the Participant’s Account shall be designated as a Retirement Account and shall be paid in a lump sum. 
  

	3.4	Additional Requirements. 

 The Deferral Election,
subject to the limitations set forth in Sections 3.1 and 3.2 hereof, shall comply with the following additional requirements, or as otherwise required by the Administrator in its sole discretion: 
 (a) Deferrals may be made in whole percentages or stated dollar amounts with such limitations as determined by the Administrator. 
 (b) The maximum amount that may be deferred each Plan Year is twenty-five percent (25%) of the Participant’s Salary and one-hundred percent
(100%) of the Participant’s Bonus, net of applicable taxes. Unless the Administrator provides otherwise, no deferrals may be made from Compensation other than Salary or Bonus. 
 (c) The minimum initial deferral period for an In-Service Account shall be two (2) years. 
  

	3.5	Matching Contribution. 

 The Employer may, in its
sole discretion, also credit to the Account of each eligible Participant who makes Deferrals a Matching Contribution in an amount determined by the Administrator; provided, that, unless the Administrator determines otherwise the amount of the
Matching Contributions for each eligible Participant for each Plan Year shall be equal to one-hundred percent (100%) of the Deferrals contributed by the Participant for such Plan Year, up to a maximum equal to: (1) four percent
(4%) of such Participant’s Compensation for such Plan Year, less (2) the amount of matching contributions made to the Company’s qualified 401(k) plan for such Plan Year on behalf of such Participant. In order to be eligible for a
Matching Contribution for a given Plan Year, a Participant must: (1) be employed by the Employer on the date the Matching Contribution is credited to the Plan, and (2) have elected to defer the maximum amount permitted under Code
Section 402(g) under the Employer’s tax-qualified Section 401(k) plan for such Plan Year. Such Matching Contribution shall be credited to such sub-account(s) as may be elected by the Participant for his or her Base Salary Deferrals,
or if no Base Salary Deferrals, then for Bonus Deferrals or if no Base Salary or Bonus Deferrals, then to the Participant’s Retirement sub-account with the shortest payment period maintained within the Participant’s Account in accordance
with Section 5.1 and procedures established by the Plan Administrator. 
  

 6 









	3.6	Employer Discretionary Contributions. 

 The Employer
reserves the right to make discretionary contributions to some or all Participants’ Accounts in such amount and in such manner as may be determined by the Employer. Such Employer Discretionary Contribution shall be credited to such
sub-account(s) as may be elected by the Participant in accordance with Sections 3.1 and 5.1 and procedures established by the Administrator, or if no such election is made by the Participant, then to such sub-account(s) as may be elected by the
Participant for his or her Base Salary Deferrals, or if no Base Salary Deferrals, then for Bonus Deferrals or if no Base Salary or Bonus Deferrals, then to the Participant’s Retirement sub-account with the shortest payment period maintained
within the Participant’s Account in accordance with Section 5.1. 
  

	3.7	Crediting of Contributions. 

 (a) Base Salary
Deferrals shall be credited to a Participant’s Account, and if applicable transferred to the Trust, as soon as administratively feasible following the close of each payroll period. Bonus Deferrals shall be credited to a Participant’s
Account, and if applicable transferred to the Trust, annually. 
 (b) Matching Contributions in respect of a Plan Year shall be credited to
the Accounts of eligible Participants, and if applicable transferred to the Trust, as of January 15 of the year subsequent to such Plan Year. 
 (c) Employer Discretionary Contributions shall be credited to a Participant’s Account, and if applicable transferred to the Trust, at such time as the Employer shall determine. 
 Article 4 - Vesting 
  

	4.1	Vesting of Deferrals. 

 A Participant shall be
one-hundred percent (100%) vested in his or her Account attributable to Deferrals and any earning or losses on the investment of such Deferrals. 
  

	4.2	Vesting of Matching Contributions. 

 A Participant
shall be one-hundred percent (100%) vested in his or her Account attributable to Matching Contributions and any earning or losses on the investment of such Matching Contributions. 
  

	4.3	Vesting of Employer Discretionary Contributions. 

 A
Participant shall have a vested right to the portion of his or her Account attributable to Employer Discretionary Contribution(s) and any earnings or losses on the investment of such Employer Discretionary Contribution(s) according to such vesting
schedule as the Employer shall determine at the time an Employer Discretionary Contribution is made. 
  

 7 









	4.4	Vesting in Event of Retirement, Disability, Death or Change-in-Control. 

 (a) A Participant who incurs a Separation from Service due to Retirement shall be fully vested in the amounts credited to his or her Account as of the date of Retirement. 
 (b) A Participant who incurs a Separation from Service due to Disability shall be fully vested in the amounts credited to his or her Account as of the
date of Disability. 
 (c) Upon a Participant’s death, the Participant shall be fully vested in the amounts credited to his or her
Account. 
 (d) Upon a Change-in-Control, all Participants shall be fully vested in the amounts credited to their Accounts as of the date of
the Change-in-Control. 
  

	4.5	Amounts Not Vested. 

 Any amounts credited to a
Participant’s Account that are not vested at the time of his or her Separation from Service shall be forfeited. 
  

	4.6	Forfeitures. 

 Any forfeitures from a
Participant’s Account shall continue to be held in the Trust, shall be separately invested and shall be used to reduce succeeding Deferrals, Employer Matching Contributions, or Employer Discretionary Contributions until such forfeitures have
been entirely so applied. If no further Contributions will be made, then such forfeitures shall be returned to the Employer. 
 Article 5 -
Accounts 
  

	5.1	Accounts. 

 The Administrator shall establish and
maintain a bookkeeping account in the name of each Participant. The Administrator shall also establish sub-accounts as provided in subsection (a) and (b), below, as elected by the Participant pursuant to Article 3. A Participant may have a
maximum of ten (10) sub-accounts at any time. 
 (a) A Participant may establish one or more Retirement Account(s) (“Retirement
sub-accounts”) by designating as such on the Participant’s Deferral Election. Each Participant’s Retirement sub-account shall be credited with Deferrals (as specified in the Participant’s Deferral Election for a given Plan Year),
any Matching Contributions allocable thereto, any Employer Discretionary Contributions for the Plan Year subject to such Deferral Election, and the Participant’s allocable share of any earnings or losses on the foregoing. Each
Participant’s Retirement sub-account shall be reduced by any distributions made plus any federal and state tax withholding, and any social security withholding tax as may be required by law. 
 (b) A Participant may elect to establish one or more In-Service Accounts (“In-Service sub-accounts”) by designating as such in the
Participant’s Deferral Election the year in which payment shall be made. Each Participant’s In-Service sub-account shall be credited with Deferrals (as specified in the Participant’s Deferral Election for a given Plan Year), any
Matching Contributions allocable thereto, any Employer Discretionary Contributions for the Plan Year 

  

 8 








 
subject to such Deferral Election, and the Participant’s allocable share of any earnings or losses on the foregoing. Each Participant’s In-Service
sub-account shall be reduced by any distributions made plus any federal and state tax withholding and any social security withholding tax as may be required by law. 
  

	5.2	Investments, Gains and Losses. 

 (a) A Participant
may direct that his or her Retirement sub-accounts and or In-Service sub-accounts established pursuant to Section 5.1 may be valued as if they were invested in one or more Investment Funds as selected by the Employer from time to time in
multiples of one percent (1%). The Employer may from time to time, at the discretion of the Administrator, change the Investment Funds for purposes of this Plan. 
 (b) The Administrator shall adjust the amounts credited to each Participant’s Account to reflect Deferrals, Matching Contributions, any Employer Discretionary Contributions, investment experience, distributions
and any other appropriate adjustments. Such adjustments shall be made as frequently as is administratively practicable. 
 (c) A Participant
may change his or her selection of Investment Funds no more than six (6) times each Plan Year with respect to his or her Account or sub-accounts by filing a new election in accordance with procedures established by the Administrator. An
election shall be effective as soon as administratively feasible following the date the change is submitted on a form prescribed by the Administrator. 
 (d) Notwithstanding the Participant’s ability to designate the Investment Fund in which his or her deferred Compensation shall be deemed invested, the Employer shall have no obligation to invest any funds in
accordance with the Participant’s election. Participants’ Accounts shall merely be bookkeeping entries on the Employer’s books, and no Participant shall obtain any property right or interest in any Investment Fund or other property
that may be held by the Trust. 
 Article 6 - Distributions 
  

	6.1	Distribution Election. 

 Each Participant shall
designate in his or her Deferral Election the form and timing of his or her distribution by indicating the type of sub-account as described under Section 5.1, and by designating the form in which payments shall be made from the choices
available under Section 6.2 and 6.3 hereof. Notwithstanding anything to the contrary contained herein provided, no acceleration of the time or schedule of payments under the Plan, or subsequent change in the time or form of distribution, shall
occur except as permitted under both this Plan and Code Section 409A. 
  

	6.2	Distributions Upon an In-Service Account Triggering Date. 

 In-Service sub-account distributions shall begin as soon as administratively feasible but no later than ninety (90) days following January 1 of the calendar year designated by the 

  

 9 








 
Participant on a properly submitted Deferral Election, and are payable in either a lump-sum payment or substantially equal annual installments, as described
in Section 6.4 below, over a period of up to five (5) years as elected by the Participant in his or her Deferral Election. If the Participant fails to properly designate the form of the distribution, the sub-account shall be paid in a
lump-sum payment. 
  

	6.3	Distributions Upon Retirement. 

 If the Participant
has a Separation from Service due to Retirement, the Participant’s Retirement sub-account(s) shall be distributed as soon as administratively feasible but no later than ninety (90) days following the Participant’s Retirement, subject
to Section 6.9 (Distributions to Specified Employees). Distribution shall be made either in a lump-sum payment or in substantially equal annual installments, as defined in Section 6.4 below, over a period of up to ten (10) years as
elected by the Participant. If the Participant fails to properly designate the form of the distribution, the sub-account shall be paid in a lump-sum payment. 
  

	6.4	Substantially Equal Annual Installments. 

 (a) The
amount of the substantially equal payments shall be determined by multiplying the Participant’s Account or sub-account by a fraction, the denominator of which in the first year of payment equals the number of years over which benefits are to be
paid, and the numerator of which is one (1). The amounts of the payments for each succeeding year shall be determined by multiplying the Participant’s Account or sub-account as of the applicable anniversary of the payout by a fraction, the
denominator of which equals the number of remaining years over which benefits are to be paid, and the numerator of which is one (1). Installment payments made pursuant to this Section 6.4 shall be made as soon as administratively feasible, but
no later than ninety (90) days, following the anniversary of the distribution event. 
 (b) For purposes of the Plan pursuant to Code
Section 409A and regulations thereunder, a series of annual installments shall be considered a single payment. 
  

	6.5	Distributions due to other Separation from Service. 

 Upon a Participant’s Separation from Service for any reason other than Retirement (including, for the avoidance of doubt, Separations from Service on account of death or Disability), all vested amounts credited to his or her Account
shall be paid to the Participant (or, in the case of death, to the Participant’s beneficiary as determined under Article 7 hereof) in a lump-sum, as soon as administratively feasible, but no later than ninety (90) days, following the date
of Separation from Service, subject to Section 6.9 (Distributions to Specified Employees). 
  

	6.6	Changes to Distribution Elections. 

 A Participant
will be permitted to elect to change the form or timing of the distribution of the balance of his or her one or more sub-accounts within his or her Account to the extent permitted and in accordance with the requirements of Code
Section 409A(a)(4)(C), including the requirement that (i) a redeferral election may not take effect until at least twelve (12) months after such election is filed with the Employer, (ii) an election to further defer a
distribution (other than a distribution upon death, Disability or an unforeseeable emergency) must result in the first 

  

 10 








 
distribution subject to the election being made at least five (5) years after the previously elected date of distribution, and (iii) any redeferral
election affecting a distribution at a fixed date must be filed with the Employer at least twelve (12) months before the first scheduled payment under the previous fixed date distribution election. Once a sub-account begins distribution, no
such changes to distributions shall be permitted. 
  

	6.7	Cash-Out Provision. 

 Notwithstanding any provision
to the contrary, and at the sole discretion of the Employer, if a Participant’s entire Account balance is less than the applicable Code Section 402(g) annual limit, the Employer may distribute the Participant’s Account in a lump sum
provided that the distribution results in the termination of the participant’s entire interest in the Plan, subject to the plan aggregation rules of Code Section 409A and regulations thereunder. 
  

	6.8	Unforeseeable Emergency. 

 The Administrator may
permit an early distribution of part or all of any deferred amounts; provided, however, that such distribution shall be made only if the Administrator, in its sole discretion, determines that the Participant, or the Participant’s beneficiary,
has experienced an Unforeseeable Emergency. An Unforeseeable Emergency is defined as a severe financial hardship resulting from an illness or accident of the Participant, the Participant’s spouse, or a dependent (as defined in Code
Section 152(a)) of the Participant, loss of the Participant’s property due to casualty or other similar extraordinary and unforeseeable circumstances arising as a result of events beyond the control of the Participant. If an Unforeseeable
Emergency is determined to exist, a distribution may not exceed the amounts necessary to satisfy such emergency plus amounts necessary to pay taxes reasonably anticipated as a result of the distribution, after taking into account the extent to which
such hardship is or may be relieved through reimbursement or compensation by insurance or otherwise or by liquidation of the Participant’s assets (to the extent the liquidation of such assets would not itself cause severe financial hardship).
Upon a distribution to a Participant under this Section 6.8, the Participant’s Deferrals shall cease and no further Deferrals shall be made for such Participant for the remainder of the Plan Year. 
  

	6.9	Distributions to Specified Employee. 

 Notwithstanding anything herein to the contrary, if any Participant is a Specified Employee upon a Separation from Service for any reason other than death, distributions to such Participant shall not commence until the first day of
the seventh month following the date of Separation from Service (or, if earlier, the date of death of the Participant). If distributions are to be made in annual installments, the second installment and all those thereafter will be made on the
applicable anniversaries of the Participant’s Separation from Service. 
  

	6.10	Exception to Separation from Service 

 At the
discretion of Employer, a third-party unrelated to Employer that acquires substantially all the assets of a subsidiary or business unit, may apply the “same desk” rule so that Participants shall not incur a Separation from Service upon the
sale or transfer of the subsidiary or business unit provided the following conditions are met: (i) the asset purchase or transfer results from bona fide arm’s length negotiations, (ii) all Participants providing services 

  

 11 








 
to the Employer prior to and after the transfer are treated consistently, and (iii) such treatment is specified in writing no later than the close date
of the asset purchase transaction. 
  

	6.11	Minimum Distribution. 

 Notwithstanding any
provision to the contrary, if the balance of a Participant’s Account or sub-account at the time of a distribution event or at the time of a scheduled installment payment is $10,000 or less, then the Participant shall be paid his or her Account
or sub-account as a single lump sum. 
  

	6.12	Separation from Service for Cause. 

 Notwithstanding
anything to the contrary contained herein, in the event the Participant has an involuntary Separation from Service for Cause, Participant shall only receive the return of their Deferrals including the Participant’s allocable share of any
earnings or losses credited on those Deferrals pursuant to Section 5.2 and subject to Section 6.9 (Distributions to Specified Employees) above. Upon a Participant’s Separation from Service for Cause, all amounts credited to
Participant’s Account amounts relating to Employer Matching Contribution(s), Employer Discretionary Contribution(s), including the Participant’s allocable share of any earnings or losses credited on the foregoing pursuant to
Section 5.2, hereinabove, shall be forfeited back to the Employer. For purposes of this Plan, “Cause” shall mean (i) engaging in willful or grossly negligent misconduct that is materially injurious to the Company and/or
affiliate, (ii) embezzlement or misappropriation of funds or property of the Company and/or affiliate, (iii) conviction of a felony or the entrance of a plea of guilty or nolo contendere to a felony, or (iv) conviction of any crime
involving fraud, dishonesty or breach of trust or the entrance of a plea of guilty or nolo contendere to such a crime. 
  

	6.13	Domestic Relations Orders 

 The Administrator may
permit such acceleration of the time or schedule of a payment under the arrangement to an individual other than a Participant as may be necessary to fulfill a domestic relations order (as defined in Code Section 414(p)(1)(B)). 
  

	6.14	Distributions Upon a Change-in-Control. 

 If elected
by a Participant at the time of initial eligibility for the Plan on a form prescribed by the Administrator, all vested amounts credited to the Participant’s Account as of the date of the Change-in-Control shall be paid in a lump sum as soon as
administratively possible, but no later than ninety (90) days, following such Change-in-Control. 
 Article 7 - Beneficiaries 

  

	7.1	Beneficiaries. 

 Each Participant may from time to
time designate one or more persons (who may be any one or more members of such person’s family or other persons, administrators, trusts, foundations or other entities) as his or her beneficiary under the Plan. Such designation shall be made in
a form prescribed by the Administrator. Each Participant may at any time and from time to time, change any previous beneficiary designation, without notice to or consent of any previously designated beneficiary, by amending his or her previous
designation in a form 

  

 12 








 
prescribed by the Administrator. If the beneficiary does not survive the Participant (or is otherwise unavailable to receive payment) or if no beneficiary is
validly designated, then the amounts payable under this Plan shall be paid to the Participant’s surviving spouse (as determined under applicable state law) or, in the event that there is no surviving spouse, to the Participant’s estate. If
more than one person is the beneficiary of a deceased Participant, each such person shall receive a pro rata share of any death benefit payable unless otherwise designated in the applicable form. If a beneficiary who is receiving benefits dies, all
benefits that were payable to such beneficiary shall then be payable to the estate of that beneficiary. 
  

	7.2	Lost Beneficiary. 

 All Participants and
beneficiaries shall have the obligation to keep the Administrator informed of their current address until such time as all benefits due have been paid. If a Participant or beneficiary cannot be located by the Administrator exercising due diligence,
then, in its sole discretion, the Administrator may presume that the Participant or beneficiary is deceased for purposes of the Plan and all unpaid amounts (net of due diligence expenses) owed to the Participant or beneficiary shall be paid
accordingly or, if a beneficiary cannot be so located, then such amounts may be forfeited. Any such presumption of death shall be final, conclusive and binding on all parties. 
 Article 8 - Funding 
  

	8.1	Unfunded Arrangement. 

 It is the express intention
of the parties hereto that this arrangement shall be unfunded for tax purposes and for purposes of Title I of the ERISA. Each Participant and beneficiary shall be required to look to the provisions of this Plan and to the Employer itself for
enforcement of any and all benefits due under this Plan, and to the extent any such person acquires a right to receive payment under this Plan, such right shall be no greater than the right of any unsecured general creditor of the Employer.

  

	8.2	Deposits in Trust. 

 Notwithstanding
Section 8.1, the Employer, in its sole and absolute discretion, may (or may not) acquire any investment product or any other instrument or otherwise invest any amount to provide the funds from which it can satisfy its obligation to make benefit
payments under this Plan. Any investment product or other item so acquired for the convenience of the Employer shall be the sole and exclusive property of the Employer (or a Trust established by the Employer) with the Employer (or the Trust) named
as sole owner and sole beneficiary thereof. To the extent that a Participant or his or her Beneficiary acquires a right to receive payments from the Employer under the provisions hereof, such right shall be no greater than the right of any unsecured
general creditor of the Employer. 
  

	8.3	Withholding of Employee Contributions; Other Tax Matters. 

 The Administrator is authorized to make any and all necessary arrangements with the Employer in order to withhold the Participant’s Deferrals under Section 3.1 hereof from his or her Compensation. The Administrator shall determine
the amount and timing of such withholding. For the avoidance of doubt, the Participant will have no discretion, and will have 

  

 13 








 
no direct or indirect election, as to whether a payment will be accelerated under this Section 8.3. The Plan may permit acceleration of the time or
schedule of a payment to a Participant to pay an amount the Participant includes in income as a result of the Plan failing to meet the requirements of Code Section 409A. Any amount distributed under this Section 8.3 will be charged against
amounts owed to the Participant and offset against future payments. 
 Article 9 - Claims Administration 
  

	9.1	General. 

 If a Participant, beneficiary or his or
her representative is denied all or a portion of an expected Plan benefit for any reason and the Participant, beneficiary or his or her representative desires to dispute the decision of the Administrator, he or she must file a written notification
of his or her claim with the Administrator. 
  

	9.2	Claims Procedure. 

 Upon receipt of any written
claim for benefits, the Administrator shall be notified and shall give due consideration to the claim presented. If any Participant or beneficiary claims to be entitled to benefits under the Plan and the Administrator determines that the claim
should be denied in whole or in part, the Administrator shall, in writing, notify such claimant within ninety (90) days of receipt of the claim that the claim has been denied. The Administrator may extend the period of time for making a
determination with respect to any claim for a period of up to ninety (90) days, provided that the Administrator determines that such an extension is necessary because of special circumstances and notifies the claimant, prior to the expiration
of the initial ninety (90) day period, of the circumstances requiring the extension of time and the date by which the Plan expects to render a decision. If the claim is denied to any extent by the Administrator, the Administrator shall furnish
the claimant with a written notice setting forth: 
 (a) the specific reason or reasons for denial of the claim; 
 (b) a specific reference to the Plan provisions on which the denial is based; 
 (c) a description of any additional material or information necessary for the claimant to perfect the claim and an explanation of why such material or
information is necessary; and 
 (d) an explanation of the provisions of this Article. 
  

	9.3	Right of Appeal. 

 A claimant who has a claim denied
wholly or partially under Section 9.2 may appeal to the Administrator for reconsideration of that claim. A request for reconsideration under this Section must be filed by written notice within sixty (60) days after receipt by the claimant
of the notice of denial under Section 9.2. 
  

 14 









	9.4	Review of Appeal. 

 Upon receipt of an appeal the
Administrator shall promptly take action to give due consideration to the appeal. Such consideration may include a hearing of the parties involved, if the Administrator feels such a hearing is necessary. In preparing for this appeal the claimant
shall be given the right to review pertinent documents and the right to submit in writing a statement of issues and comments. After consideration of the merits of the appeal the Administrator shall issue a written decision which shall be binding on
all parties. The decision shall specifically state its reasons and pertinent Plan provisions on which it relies. The Administrator’s decision shall be issued within sixty (60) days after the appeal is filed, except that the Administrator
may extend the period of time for making a determination with respect to any claim for a period of up to sixty (60) days, provided that the Administrator determines that such an extension is necessary because of special circumstances and
notifies the claimant, prior to the expiration of the initial sixty (60) day period, of the circumstances requiring the extension of time and the date by which the Plan expects to render a decision. 
  

	9.5	Designation. 

 The Administrator may designate any
other person of its choosing to make any determination otherwise required under this Article. Any person so designated shall have the same authority and discretion granted to the Administrator hereunder. 
 Article 10 - General Provisions 
  

	10.1	Administrator. 

 (a) The Administrator is expressly
empowered to limit the amount of Compensation that may be deferred; to deposit amounts into the Trust in accordance with Section 8.2 hereof; to interpret the Plan, and to determine all questions arising in the administration, interpretation and
application of the Plan; to employ actuaries, accountants, counsel, and other persons it deems necessary in connection with the administration of the Plan; to request any information from the Employer it deems necessary to determine whether the
Employer would be considered insolvent or subject to a proceeding in bankruptcy; and to take all other necessary and proper actions to fulfill its duties as Administrator. 
 (b) The Administrator shall not be liable for any actions by it hereunder, unless due to its own negligence, willful misconduct or lack of good faith.

 (c) The Administrator shall be indemnified and saved harmless by the Employer from and against all personal liability to which it may be
subject by reason of any act done or omitted to be done in its official capacity as Administrator in good faith in the administration of the Plan and Trust, including all expenses reasonably incurred in its defense in the event the Employer fails to
provide such defense upon the request of the Administrator. The Administrator is relieved of all responsibility in connection with its duties hereunder to the fullest extent permitted by law, short of breach of duty to the beneficiaries. 

 

 15 









	10.2	No Assignment. 

 Benefits or payments under this
Plan shall not be subject in any manner to anticipation, alienation, sale, transfer, assignment, pledge, encumbrance, attachment, or garnishment by creditors of the Participant or the Participant’s beneficiary, whether voluntary or involuntary,
and any attempt to so anticipate, alienate, sell, transfer, assign, pledge, encumber, attach or garnish the same shall not be valid, nor shall any such benefit or payment be in any way liable for or subject to the debts, contracts, liabilities,
engagement or torts of any Participant or beneficiary, or any other person entitled to such benefit or payment pursuant to the terms of this Plan, except to such extent as may be required by law. If any Participant or beneficiary or any other person
entitled to a benefit or payment pursuant to the terms of this Plan becomes bankrupt or attempts to anticipate, alienate, sell, transfer, assign, pledge, encumber, attach or garnish any benefit or payment under this Plan, in whole or in part, or if
any attempt is made to subject any such benefit or payment, in whole or in part, to the debts, contracts, liabilities, engagements or torts of the Participant or beneficiary or any other person entitled to any such benefit or payment pursuant to the
terms of this Plan, then such benefit or payment, in the discretion of the Administrator, shall cease and terminate with respect to such Participant or beneficiary, or any other such person. 
  

	10.3	No Employment Rights. 

 Participation in this Plan
shall not be construed to confer upon any Participant the legal right to be retained in the employ of the Employer, or give a Participant or beneficiary, or any other person, any right to any payment whatsoever, except to the extent of the benefits
provided for hereunder. Each Participant shall remain subject to discharge to the same extent as if this Plan had never been adopted. 
  

	10.4	Incompetence. 

 If the Administrator determines that
any person to whom a benefit is payable under this Plan is incompetent by reason of physical or mental disability, the Administrator shall have the power to cause the payments becoming due to such person to be made to another for his or her benefit
without responsibility of the Administrator or the Employer to see to the application of such payments. Any payment made pursuant to such power shall, as to such payment, operate as a complete discharge of the Employer, the Administrator and the
Trustee. 
  

	10.5	Identity. 

 If, at any time, any doubt exists as to
the identity of any person entitled to any payment hereunder or the amount or time of such payment, the Administrator shall be entitled to hold such sum until such identity or amount or time is determined or until an order of a court of competent
jurisdiction is obtained. The Administrator shall also be entitled to pay such sum into court in accordance with the appropriate rules of law. Any expenses incurred by the Employer, Administrator, and Trust incident to such proceeding or litigation
shall be charged against the Account of the affected Participant. 
  

	10.6	Other Benefits. 

 The benefits of each Participant
or beneficiary hereunder shall be in addition to any benefits paid or payable to or on account of the Participant or beneficiary under any other pension, disability, annuity or retirement plan or policy whatsoever. 
  

 16 









	10.7	Expenses. 

 All expenses incurred in the
administration of the Plan, whether incurred by the Employer or the Plan, shall be paid by the Employer. 
  

	10.8	Insolvency. 

 Should the Employer be considered
insolvent (as defined by the Trust), the Employer, through its Board and chief executive officer, shall give immediate written notice of such to the Administrator of the Plan and the Trustee. Upon receipt of such notice, the Administrator or Trustee
shall cease to make any payments to Participants who were Employees of the Employer or their beneficiaries and shall hold any and all assets attributable to the Employer for the benefit of the general creditors of the Employer. 
  

	10.9	Amendment or Modification. 

 The Employer may, at
any time, in its sole discretion, amend or modify the Plan in whole or in part, except that no such amendment or modification shall have any retroactive effect to reduce any amounts allocated to a Participant’s Accounts, and provided that such
amendment or modification complies with Codes Section 409A and related regulations thereunder. 
  

	10.10	Plan Suspension. 

 The Employer further reserves the
right to suspend the Plan in whole or in part, except that no such suspension shall have any retroactive effect to reduce any amounts allocated to a Participant’s Accounts, and provided that that distribution of the vested Participant Accounts
shall not be accelerated but shall be paid at such time and in such manner as determined under the terms of the Plan immediately prior to suspension as if the Plan had not been suspended. 
  

	10.11	Plan Termination. 

 The Employer further reserves
the right to terminate the Plan in whole or in part, in the following manner, except that no such termination shall have any retroactive effect to reduce any amounts allocated to a Participant’s Accounts, and provided that such termination
complies with Codes Section 409A and related regulations thereunder. The Employer, in its sole discretion, may terminate the Plan and distribute all vested Participants’ Accounts no earlier than twelve (12) calendar months from the
date of the Plan termination and no later than twenty-four (24) calendar months from the date of the Plan termination, provided however that all other similar arrangements are also terminated by the Employer and no other similar arrangements
are adopted by the Employer within a three year period from the date of termination. 
  

	10.12	Plan Termination due to a Change-in-Control. 

 Notwithstanding Section 10.11, the Employer may decide, in its discretion, to terminate the Plan in the event of a Change-in-Control and distribute all vested Participants Account balances no earlier than thirty (30) days prior to
the Change-in-Control and no later than twelve (12) months after the effective date of the Change-in-Control, provided however that the Employer terminates all other similar arrangements. Any corporation or other business organization that is a
successor to the Employer by reason of a Change-in-Control shall have the right to become a party to the Plan by appropriate entity action. If within thirty (30) days from 

  

 17 








 
the effective date of the Change-in-Control such new entity does not become a party hereto, as above provided, the full amount of the Participant’s
Account shall become immediately distributable to the Participant pursuant to this subsection. 
  

	10.13	Construction. 

 All questions of interpretation,
construction or application arising under or concerning the terms of this Plan shall be decided by the Administrator, in its sole and final discretion, whose decision shall be final, binding and conclusive upon all persons. 
  

	10.14	Governing Law. 

 This Plan shall be governed by,
construed and administered in accordance with the applicable provisions of ERISA, Code Section 409A, and any other applicable federal law, provided, however, that to the extent not preempted by federal law this Plan shall be governed by,
construed and administered under the laws of the State of Delaware, other than its laws respecting choice of law. 
  

	10.15	Severability. 

 If any provision of this Plan is
held invalid or unenforceable, its invalidity or unenforceability shall not affect any other provision of this Plan and this Plan shall be construed and enforced as if such provision had not been included therein. If the inclusion of any Employee
(or Employees) as a Participant under this Plan would cause the Plan to fail to comply with the requirements of sections 201(2), 301(a)(3) and 401(a)(1) of ERISA, or Code Section 409A, then the Plan shall be severed with respect to such
Employee or Employees, who shall be considered to be participating in a separate arrangement. 
  

	10.16	Headings. 

 The Article headings contained herein
are inserted only as a matter of convenience and for reference and in no way define, limit, enlarge or describe the scope or intent of this Plan nor in any way shall they affect this Plan or the construction of any provision thereof. 
  

	10.17	Terms. 

 Capitalized terms shall have meanings as
defined herein. Singular nouns shall be read as plural, masculine pronouns shall be read as feminine, and vice versa, as appropriate. 
 The remainder of this page was intentionally left blank. 
  

 18 








 IN WITNESS WHEREOF, CombinatoRx, Incorporated has caused this instrument to be executed by its duly
authorized officer, effective as of this 1st day of December, 2007. 
  

			
	CombinatoRx, Incorporated
		
	By:	 	 /s/ Robert Forrester

		
	Title:	 	EVP and Chief Financial Officer


  

			
	ATTEST:
		
	By:	 	 /s/ Jason F. Cole

		
	Title:	 	SVP and General Counsel

  

 19