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                                                                 Exhibit 10.31

                            COMBINATORX, INCORPORATED

                               FOUNDER'S AGREEMENT

     This Founder's Agreement (this "Agreement") is made and entered into as of
this 26th day of January, 2001, by and between CombinatoRx, Incorporated, a
Delaware corporation (the "Company") and Brent Stockwell (the "Founder").

                                   RECITALS '

     WHEREAS, the Founder is now the owner of 9,500 shares of Common Stock of
the Company of which 2,375 shares have vested and are not subject to the
Repurchase Option (as defined below) and of which 7,125 shares (the "Shares")
are subject to the Repurchase Option pursuant to the terms of this Agreement.

     WHEREAS, the parties desire to enter into this Agreement in connection
with, and as a condition precedent to, the issuance and sale of shares of the
Company's Series B Preferred Stock to certain investors.

     NOW, THEREFORE, in consideration of the premises and for other good and
valuable consideration, the receipt and sufficiency of which are hereby
acknowledged, the parties hereto agree as follows:

     1.   REPURCHASE OPTION.

          (a)  In the event that the Founder's employment with or services to
the Company are terminated other than as a result of a Termination Event before
all of the Shares are released from the Repurchase Option of the Company (as
provided in Section 2), the Company shall have, upon the date of such
termination (as reasonably fixed and determined by the Company), an irrevocable,
exclusive option (the "Repurchase Option") for a period of ninety (90) from such
date to repurchase all or any portion of the Unreleased Shares (as defined in
Section 2) at such time, at the original purchase price per share (the
"Repurchase Price"). The Repurchase Option shall be exercised by the Company by
written notice to the Founder or the Founder's executor (with a copy to the
Escrow Holder) and, at the Company's option, (i) by delivery to the Founder or
the Founder's executor with such notice of a check in the amount of the
Repurchase Price for the Shares being repurchased, (ii) by cancellation by the
Company of an amount of the Founder's indebtedness to the Company equal to the
Repurchase Price for the Shares being repurchased or (iii) by a combination of
(i) and (ii) so that the combined payment and cancellation of indebtedness
equals such Repurchase Price. Upon delivery of such notice and the payment of
the Repurchase Price as described above, the Company shall become the legal and
beneficial owner of the Shares being repurchased and all rights and interests
therein or relating thereto, and the Company shall have the right to retain and
transfer to its own name the number of Shares being repurchased by the Company.
A "Termination Event" shall mean any of the following events: (x) the death of
the Founder, (y) the Founder's election to terminate his consulting relationship
with the Company as a direct result of the Company's material reduction

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in the nature of the Founder's responsibilities regarding his consulting
position with the Company or (z) the Company's election to terminate the
Founder's consulting relationship with the Company other than in connection with
any of the following relating to the Founder: (1) conviction of, the indictment
for, or the entering of a guilty plea or plea of no contest with respect to, a
felony, any act involving moral turpitude, or a misdemeanor where imprisonment
is a possible punishment, (2) commission of any act of theft, fraud or
dishonesty, (3) improper disclosure of the Company's confidential or proprietary
information, (4) any action involving moral turpitude which has a detrimental
effect on the Company's reputation or business, (5) failure or inability to
perform any reasonably assigned duties after written notice from the company of,
and a reasonable opportunity to cure, such failure or inability, (6) any breach
of this Agreement or any employment, consulting, advisory or other agreement
with the Company, (7) a course of conduct amounting to gross incompetence, (8)
chronic and unexcused absenteeism, (9) unlawful appropriation of a business
opportunity, or (10) misconduct in connection with the performance of any duties
or responsibilities, including, without limitation, misappropriation of funds or
property of the Company, securing or attempting to secure personally any profit
in connection with any transaction entered into on behalf of the Company,
misrepresentation to the Company, or any violation of law or regulations on
Company premises or to which the Company is subject.

     2.   RELEASE OF SHARES FROM REPURCHASE OPTION.

          (a)  One thirty-sixth (1/36) of the Shares shall be released from the
Repurchase Option on the last day of each full calendar month following January
25, 2001 until all the Shares have been released from the Repurchase Option
provided that, except as set forth in the immediately following sentence, in
each case that the Founder's services as an employee of or consultant to the
Company have not been terminated prior to the date of any such release. In the
event that a Termination Event has occurred, all of the Unreleased Shares shall
be immediately released from the Company's Repurchase Option.

          (b)  Any of the Shares which have not yet been released from the
Repurchase Option are referred to herein as "Unreleased Shares." The Shares
which have been released from the Repurchase Option shall be delivered to the
Founder at the Founder's request.

          (c)  This Agreement shall not confer upon the Founder any right with
respect to continuation of employment by the Company, nor shall it interfere
with or affect in any manner the right or power of the Company, or a parent or
subsidiary of the Company, to terminate the Founder's employment at any time or
for any reason, with or without cause, which right is hereby reserved.

     3.   RESTRICTION ON TRANSFER. Except for the escrow described in Section 4
or the transfer of the Shares to the Company or its assignees as contemplated by
this Agreement, none of the Shares or any beneficial interest therein shall be
transferred, encumbered or otherwise disposed of in any way until the release of
such Shares from the Repurchase Option in accordance with the provisions of this
Agreement.

                                        2
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     4.   ESCROW OF SHARES.

          (a)  The Shares shall be held by Rubin and Rudman LLP (the "Escrow
Holder"), along with a stock assignment executed by the Founder in blank, until
the expiration of the Repurchase Option as set forth above.

          (b)  The Escrow Holder is hereby directed to permit transfer of the
Shares only in accordance with this Agreement or instructions signed by both
parties. In the event further instructions are desired by the Escrow Holder, the
Escrow Holder shall be entitled to rely upon directions executed by a majority
of the authorized number of the Company's Board of Directors. The Escrow Holder
shall have no liability for any act or omission hereunder while acting in good
faith in the exercise of the Escrow Holder's own judgment.

          (c)  If the Company or any assignee exercises the Repurchase Option
hereunder, the Escrow Holder, upon receipt of written notice of such option
exercise from the proposed transferee, shall take all steps necessary to
accomplish such transfer.

          (d)  When the Repurchase Option has been exercised or expires
unexercised or a portion of the Shares has been released from such Repurchase
Option, upon Founder's request the Escrow Holder shall promptly cause a new
certificate to be issued for such released Shares and shall deliver such
certificate to the Founder.

          (e)  Subject to the terms hereof, the Founder shall have all the
rights of a stockholder with respect to the Shares while they are held in
escrow, including, without limitation, the right to vote the Shares and receive
any dividends declared thereon. If, from time to time during the term of the
Repurchase Option, there is any stock dividend, stock split or other change in
the Shares, any and all new, substituted or additional securities to which the
Founder is entitled by reason of the Founder's ownership of the Shares subject
to the Repurchase Option shall be immediately subject to this escrow, deposited
with the Escrow Holder and included thereafter as "Shares" for purposes of this
Agreement and the Repurchase Option.

     5.   MARKET STAND-OFF AGREEMENT. The Founder hereby agrees that, during the
period of duration specified by the Company and an underwriter of Common Stock
or other securities of the Company, following the effective date of a
registration statement of the Company filed under the Securities Act of 1933, as
amended, he 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 him at
any time during such period except Common Stock included in such registration

     6.   LEGENDS. The share certificate evidencing the Shares issued hereunder
shall be endorsed with the following legends:

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          (a)  "These securities have not been registered under the Securities
Act of 1933, as amended. They may not be sold, offered for sale, pledged or
hypothecated in the absence of a registration statement in effect with respect
to the securities under such Act or an opinion of counsel satisfactory to the
Company that such registration is not required or unless sold pursuant to Rule
144 of such Act."

          (b)  "The shares represented by this certificate may be transferred
only in accordance with the terms of an agreement between the Company and the
stockholder, a copy of which is on file with the Secretary of the Company."

               (c)  Any legend required by applicable securities laws including,
without limitation, any legend required by the General Corporation Law of the
State of Delaware.

     7.   ADJUSTMENT FOR STOCK. All references to the number of Shares and the
purchase price of the Shares in this Agreement shall be appropriately adjusted
to reflect any stock split, stock dividend or other change in the Shares which
may be made by the Company after the date of this Agreement.

     8.   GENERAL PROVISIONS.

          (a)  This Agreement shall be governed by and construed under the laws
of the Commonwealth of Massachusetts without regard to the principles of
conflicts of law.

          (b)  This Agreement and the documents referred to herein constitute
the entire agreement among the parties regarding the subject matters hereof and
thereof.

          (c)  Any provision of this Agreement may be amended or the observance
thereof may be waived (either generally or specifically and either retroactively
or prospectively), only by an instrument in writing executed by the Company and
the Founder. Any amendment or waiver so effected shall be binding upon the
Founder, the Company and any assignee or successor of any such party.

          (d)  Any notices required in connection with this Agreement shall be
in writing and shall be deemed effectively given: (i) upon personal delivery to
the party to be notified, (ii) five (5) days after having been sent by
registered or certified mail, return receipt requested, postage prepaid, or
(iii) one (1) day after deposit with a nationally recognized overnight courier,
specifying next day delivery, with written notification of receipt. All notices
shall be addressed to the applicable party to such party's address appearing on
the signature page to this Agreement or at such address as such party may
designate by ten (10) days advance written notice to the other parties hereto.

          (e)  All covenants and agreements hereunder shall inure to the benefit
of, and be enforceable by, the Company's successors and assigns. The rights and
obligations of the Founder under this Agreement may only be assigned with the
prior written consent of the Company.

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          (f)  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.

          (g)  The Founder agrees upon request to execute any further documents
or instruments necessary or desirable to carry out the purposes or intent of
this Agreement.

          (h)  The titles and subtitles used in this Agreement are used for
convenience only and are not to be considered in construing or interpreting this
Agreement.

          (i)  In the event that one or more of the provisions of this Agreement
are held to be unenforceable under applicable law, such provision shall be
excluded from this Agreement and the balance of the Agreement shall be
interpreted as if such provision were so excluded and shall be enforceable in
accordance with its terms.

          (j)  No waivers of any breach of this Agreement extended by any party
hereto to any other party shall be construed as a waiver of any rights or
remedies of any other party hereto or with respect to any subsequent breach.

          (k)  THE FOUNDER ACKNOWLEDGES AND AGREES THAT THE VESTING OF SHARES
PURSUANT TO SECTION 2 HEREOF IS EARNED ONLY BY CONTINUING SERVICE TO THE
COMPANY. THE FOUNDER FURTHER ACKNOWLEDGES AND AGREES THAT THIS AGREEMENT, THE
TRANSACTIONS CONTEMPLATED HEREUNDER AND THE VESTING SCHEDULE SET FORTH HEREIN DO
NOT CONSTITUTE AN EXPRESS OR IMPLIED PROMISE OF CONTINUED ENGAGEMENT AS AN
EMPLOYEE FOR THE VESTING PERIOD, FOR ANY PERIOD, OR AT ALL, AND SHALL NOT
INTERFERE WITH THE FOUNDER'S RIGHT OR THE COMPANY'S RIGHT TO TERMINATE THE
FOUNDER'S EMPLOYMENT RELATIONSHIP AT ANY TIME, WITH OR WITHOUT CAUSE.

          (l)  The Founder has reviewed this Agreement in its entirety, has had
an opportunity to obtain the advice of counsel prior to executing this Agreement
and fully understands all provisions of the Agreement. The Founder agrees to
notify the Company upon any change in the residence address indicated below.

                [Remainder of the page intentionally left blank.]

                                        5
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     IN WITNESS WHEREOF, the parties have executed this Agreement as of the date
first above written.

                                     COMPANY:

                                         COMBINATORX, INCORPORATED

                                         By: /s/ Alexis Borisy
                                             -----------------------------------
                                             Name:
                                             Title:

                                         Address:     801 Albany Street
                                                      Suite G02
                                                      Boston, MA 02118

                                     FOUNDER:

                                         /s/ Brent Stockwell
                                         ---------------------------------------
                                         Name: Brent Stockwell, Ph.D.
                                         Address:

                                     ESCROW HOLDER:

                                         RUBIN AND RUDMAN LLP

                                         By:/s/ Peter B. Finn
                                            ------------------------------------
                                            Name:
                                            Title:
                                            Address: 50 Rowes Wharf
                                                     Boston, MA 02110-3319

                    [SIGNATURE PAGE TO FOUNDER'S AGREEMENT]

<Page>

                      ASSIGNMENT SEPARATE FROM CERTIFICATE

     FOR VALUE RECEIVED, _______________ hereby sells, assigns and transfers
unto ________________ (_______________) shares of the Common Stock of
CombinatoRx, Incorporated, a Delaware corporation (the "Company") standing in
the name of ____________________ on the books of said corporation represented by
Certificate No. ___________ herewith and do hereby irrevocably constitute and
appoint Rubin and Rudman LLP, attorney, to transfer the said stock on the books
of the within named corporation with full power of substitution in the premises.

     This Assignment Separate from Certificate may be used only in accordance
with the Founder's Agreement by and between the Company and the undersigned
dated January 26, 2001.

Dated: January 26, 2001

                                 Signature: /s/ Brent Stockwell
                                           ------------------------------
                                           Name: Brent Stockwell, Ph.D.

INSTRUCTION: PLEASE DO NOT FILL IN ANY BLANKS OTHER THAN THE SIGNATURE LINE. THE
PURPOSE OF THIS ASSIGNMENT IS TO ENABLE THE COMPANY TO EXERCISE ITS "REPURCHASE
OPTION" SET FORTH IN THE AGREEMENT WITHOUT REQUIRING ADDITIONAL SIGNATURES ON
THE PART OF THE FOUNDER.QuickLinks
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Exhibit 10.99  

 
 

SIXTH AMENDMENT TO
  GAS SALES AGREEMENT    
    

This Sixth Amendment to Gas Sales Agreement ("Amendment") is executed as of December 31, 2004, by Tipperary Oil & Gas (Australia) Pty Ltd (ACN 077 536 871)
of GPO Box 1100, Brisbane, Queensland, Australia 4001 ("Seller"), and QUEENSLAND FERTILISER ASSETS LIMITED (ACN 011 062 294) of 76 Arthur Street, Roma, Queensland, Australia ("Buyer"). 

WITNESSETH:  

	A.
	The
Seller and Buyer have previously delivered Gas Sales Agreement dated September 28, 2001, as amended by Amendment to Gas Sales Agreement dated as of May 30, 2002,
Second Amendment to Gas Sale Agreement dated as of September 1, 2002, Third Amendment to Gas Sale Agreement dated as of January 1, 2003, Fourth Amendment to Gas Sale Agreement dated as
of March 31, 2003 and Fifth Amendment to Gas Sale Agreement dated as of June 30, 2003 (collectively, the "Original Agreement") governing the sale and supply of Gas to Buyer subject to
the terms and conditions set forth therein including, without limitation, the Seller and the Buyer obtaining necessary financing commitments, under terms reasonably acceptable to each of them, by
December 31, 2003 for (a) Buyer to construct and commission the Plant and the Pipeline between December 31, 2003 and the Commencement Date and (b) Seller to drill and
complete the number of wells, and install laterals and compressors, as Seller reasonably deems necessary between December 31, 2003 and the Commencement Date to deliver the ACQ to the Delivery
Point and meet Pipeline Pressure requirements; and

	B.
	The
Seller and Buyer have agreed, subject to the terms and conditions set forth below, to amend the Original Agreement to (1) extend the date for Seller and Buyer to obtain
their respective financing commitments to March 31, 2004 and (2) otherwise modify the Original Agreement as set forth herein.

NOW,
THEREFORE, for a sufficient consideration received by each, the Seller and Buyer agree to amend the Original Agreement as follows. 

	1.
	Definitions. The definition of Commencement Date in the Original Agreement is hereby
amended and replaced in its entirety as set forth below. 

"Commencement
Date" means the later of: 

	(a)
	1
September 2006; or

	(b)
	the
date after 1 September 2006 on which the Buyer takes the first delivery of Gas from the Seller under this Agreement pursuant to the notice given under  Clause 2.4; 

provided that, if Buyer has not previously taken the first delivery of Gas from the Seller under Subparagraph (b) above, the Commencement Date
shall be deemed to occur on 1 January 2007." 

	2.
	Sale and Purchase. Section 2.1, the preamble of  Section 2.2 and Section 2.4 of the Original Agreement, each stating conditions precedent
to Seller's and Buyer's obligations under the Original Agreement, are hereby amended and replaced in their entirety as set forth below. 

"2.1
The obligations of the Parties under the Agreement, other than their obligations under Clauses 17, 20 and 24, are subject to and do not become
binding unless: 

	(a)
	Buyer:
(i) establishes and maintains its creditworthiness to the reasonable satisfaction of the Seller, and (ii) the Buyer has in place the necessary financing
commitments, under terms 

1

 

reasonably
acceptable to Buyer and Seller, that will foreseeably allow Buyer to construct and commission the Plant and the Pipeline between March 31, 2004 and the Commencement Date. If these
conditions precedent are not satisfied by March 31, 2004, then this Agreement will terminate (except for Clauses 17, 20 and 24 and the
enforcement of any right or claim which arises thereunder), unless the Seller agrees in writing to extend the time required to meet these conditions. 

	(b)
	Seller
has in place the necessary financing commitments, under terms reasonably acceptable to Buyer and Seller, that will foreseeably allow Seller to drill and complete the number of
wells, to install laterals and compressors, as Seller reasonably deems necessary between March 31, 2004 and the Commencement Date to deliver the ACQ to the Delivery Point and meet Pipeline
Pressure requirements. If these conditions precedent are not satisfied by March 31, 2004, then this Agreement will terminate (except for Clauses 17, 20 and
24 and the enforcement of any right of claim which arises thereunder), unless Buyer agrees in writing to extend the time required to meet this condition." 

"2.2
In addition to the conditions in Clause 2.1, Buyer shall begin actual construction of the Plant by September 1, 2004, and diligently
prosecute actual construction of the Plant and the Pipeline thereafter in an orderly and prudent manner through and until the Commencement Date." 

"2.4
The Buyer must deliver written notice to the Seller not less that forty-five (45) Business Days' before the Day on which the Buyer intends to take the first delivery of Gas
from the Seller under this Agreement; provided that Seller shall have no obligation to supply Gas to Buyer before 1 June 2006." 

	3.
	Authority, Effect and Governing Law. Section 20.1 (a),
containing a representation and warranty regarding Seller's and Buyer's corporate proceedings with respect to the Original Agreement, is hereby amended and replaced in its entirety as set forth below. 

"20.1
Each Party represents and warrants to the other Party now and at all times during the Term: 

	(a)
	It
is a company duly incorporated under the laws of Queensland and has the power and authority to enter into this Agreement and will have undertaken and complied with the necessary
corporate proceedings to ensure this Agreement is enforceable and binding on it or before March 31, 2004 (unless otherwise terminated on or before that date);"

 

	4.
	Capitalized Terms. All capitalized terms shall have the meaning assigned to them in the Original Agreement,
except as added, amended or otherwise restated herein or unless the context clearly requires otherwise. In addition: references in the Original Agreement to the "Agreement," "hereof", "herein" and
words of similar import shall be deemed to be references to the Original Agreement as amended hereby.

	5.
	Representations. The Seller and Buyer respectively represent and warrant that all of the representations and
warranties contained in the Original Agreement (and any certificates and documents executed pursuant thereto or contemplated thereby) are true and correct in all material respects on and as of the
effective date of this Amendment.

	6.
	Conflicts and Continuation. In the event that this Amendment conflicts or is
inconsistent with the Original Agreement, this Amendment shall control. Except as specifically amended herein, all of the terms and conditions of the Original Agreement (and any certificates and
documents executed pursuant thereto or contemplated thereby) shall remain in full force and effect in accordance with their respective terms.

	7.
	Severability. In the event any one or more provisions contained in the Original Agreement or this Amendment
should be held to be invalid, illegal or unenforceable in any respect, the validity, enforceability and legality of the remaining provisions contained herein and therein shall not be 

2

 

affected
in any way or impaired thereby and shall be enforceable in accordance with their respective terms. 

	8.
	Acknowledgment. The Seller and Buyer respectively ratify and confirm that the Original
Agreement (and any certificates and documents executed pursuant thereto or contemplated thereby) remain in full force and effect in accordance with their respective terms, except as amended hereby.
The representatives of the Seller and Buyer executing this Amendment each represent and warrant to the others that they are duly appointed agents or officers of the party to the Original Agreement as
designated in the signature lines below, they have full power and authority to execute and deliver this Amendment on behalf of the party to the Original Agreement as designated below, they have
obtained all corporate or other authorizations as may be applicable to each of them. 

EXECUTED
as an agreement. 

	THE COMMON SEAL of TIPPERARY OIL & GAS (Australia)	 	)
	Pty LTD (ACN 077 536 871 was duly affixed to this document in	 	)
	accordance with its articles of association in the presence of:	 	)

	

/s/  RICHARD A. BARBER      
 Signature of Secretary	
 	

/s/  DAVID L. BRADSHAW      
 Signature of Director
	

RICHARD A. BARBER
 Name of Secretary—please print	

 	

DAVID L. BRADSHAW
 Name of Director—please print

[Remainder
of this page intentionally left blank] 

3

 

	THE COMMON SEAL OF QUEENSLAND	 	)
	FERTILIZER ASSETS LIMITED (ACN 011 062 294)	 	)
	was duly affixed to this document in accordance	 	)
	with its Articles of Association in the presence of:	 	)

	

/s/  H. J. K. HOWES      
 Signature of Secretary	
 	

/s/  JOHN F. BABBITT      
 Signature of Director
	

H. J. K. HOWES
 Name of Secretary—please print	
 	

JOHN F. BABBITT
 Name of Director—please print

4

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SIXTH AMENDMENT TO GAS SALES AGREEMENT

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