NONSTATUTORY STOCK OPTION AGREEMENT DAVID SCHEER



 Exhibit 10.1 
 Achillion Pharmaceuticals, Inc. 
 Nonstatutory Stock Option Agreement  
 Granted Under 2006 Stock Incentive Plan 
  

	1.	Grant of Option. 

 This agreement evidences the
grant by Achillion Pharmaceuticals, Inc. a Delaware corporation (the “Company”), on December 19, 2006 (the “Grant Date”) to David Scheer, a director of the Company (the “Participant”), of an option to purchase, in
whole or in part, on the terms provided herein and in the Company’s 2006 Stock Incentive Plan (the “Plan”), a total of 15,000 shares (the “Shares”) of common stock, .001 par value per share, of the Company (“Common
Stock”) at $14.75 per Share. Unless earlier terminated, this option shall expire at 5:00 p.m., Eastern time, on December 18, 2016 (the “Final Exercise Date”). 
 It is intended that the option evidenced by this agreement shall not be an incentive stock option as defined in Section 422 of the Internal Revenue
Code of 1986, as amended, and any regulations promulgated thereunder (the “Code”). Except as otherwise indicated by the context, the term “Participant”, as used in this option, shall be deemed to include any person who acquires
the right to exercise this option validly under its terms. 
  

	2.	Vesting Schedule. 

 This option will become
exercisable (“vest”) as to 100% of the original number of Shares on the Grant Date. 
 The right of exercise shall be cumulative so
that to the extent the option is not exercised in any period to the maximum extent permissible it shall continue to be exercisable, in whole or in part, with respect to all Shares for which it is vested until the earlier of the Final Exercise Date
or the termination of this option under Section 3 hereof or the Plan. 
 3. Exercise of Option. 
 (a) Form of Exercise. Each election to exercise this option shall be in writing, signed by the Participant, and received by the Company at its
principal office, accompanied by this agreement, and payment in full in the manner provided in the Plan. A form of Notice of Stock Option Exercise is attached as Exhibit A. The Participant may purchase less than the number of shares covered
hereby, provided that no partial exercise of this option may be for any fractional share or for fewer than ten whole shares. 
 (b)
Continuous Relationship with the Company Required. Except as otherwise provided in this Section 3, this option may not be exercised unless the Participant, at the time he or she exercises this option, is, and has been at all times since
the Grant Date, an employee or officer or director of, or consultant or advisor to, the Company or any other entity the employees, officers, directors, consultants, or advisors of which are eligible to receive option grants under the Plan (an
“Eligible Participant”). 
  







 (c) Termination of Relationship with the Company. If the Participant ceases to be an Eligible
Participant for any reason, then, except as provided in paragraphs (d) and (e) below, the right to exercise this option shall terminate three months after such cessation (but in no event after the Final Exercise Date), provided that
this option shall be exercisable only to the extent that the Participant was entitled to exercise this option on the date of such cessation. Notwithstanding the foregoing, if the Participant, prior to the Final Exercise Date, violates the
non-competition or confidentiality provisions of any employment contract, confidentiality and nondisclosure agreement or other agreement between the Participant and the Company, the right to exercise this option shall terminate immediately upon
written notice to the Participant from the Company describing such violation. 
 (d) Exercise Period Upon Death or Disability. If the
Participant dies or becomes disabled (within the meaning of Section 22(e)(3) of the Code) prior to the Final Exercise Date while he or she is an Eligible Participant and the Company has not terminated such relationship for “cause” as
specified in paragraph (e) below, this option shall be exercisable, within the period of one year following the date of death or disability of the Participant, by the Participant (or in the case of death by an authorized transferee),
provided that this option shall be exercisable only to the extent that this option was exercisable by the Participant on the date of his or her death or disability, and further provided that this option shall not be exercisable after the
Final Exercise Date. 
 (e) Termination for Cause. If, prior to the Final Exercise Date, the Participant’s employment or other
relationship with the Company is terminated by the Company for Cause (as defined below), the right to exercise this option shall terminate immediately upon the effective date of such termination of employment or other relationship. If the
Participant is party to an employment, consulting or severance agreement with the Company that contains a definition of “cause” for termination of employment or other relationship, “Cause” shall have the meaning ascribed to such
term in such agreement. Otherwise, “Cause” shall mean willful misconduct by the Participant or willful failure by the Participant to perform his or her responsibilities to the Company (including, without limitation, breach by the
Participant of any provision of any employment, consulting, advisory, nondisclosure, non-competition or other similar agreement between the Participant and the Company), as determined by the Company, which determination shall be conclusive. The
Participant shall be considered to have been discharged for “Cause” if the Company determines, within 30 days after the Participant’s resignation, that discharge for cause was warranted. 
  

	4.	Withholding. 

 No Shares will be issued pursuant to
the exercise of this option unless and until the Participant pays to the Company, or makes provision satisfactory to the Company for payment of, any federal, state or local withholding taxes required by law to be withheld in respect of this option.

  

	5.	Nontransferability of Option. 

 This option may not
be sold, assigned, transferred, pledged or otherwise encumbered by the Participant, either voluntarily or by operation of law, except by will or the laws of descent 










 
and distribution, and, during the lifetime of the Participant, this option shall be exercisable only by the Participant. 
  

	6.	Provisions of the Plan. 

 This option is subject to
the provisions of the Plan, a copy of which is furnished to the Participant with this option. 
 IN WITNESS WHEREOF, the Company has caused
this option to be executed under its corporate seal by its duly authorized officer. This option shall take effect as a sealed instrument. 
  
 Achillion Pharmaceuticals, Inc. 
 Dated:
December 26, 2006 
 By: /s/ Mary Kay Fenton 
         Name: Mary Kay Fenton 
         Title: Chief Financial Officer 







 PARTICIPANT’S ACCEPTANCE 
 The undersigned hereby accepts the foregoing option and agrees to the terms and conditions thereof. The undersigned hereby acknowledges receipt of a copy
of the Company’s 2006 Stock Incentive Plan. 
 PARTICIPANT: 
 /s/ David
Scheer                     
 Address:                                

               _______________ 
  
  







 Exhibit A 
 NOTICE OF STOCK OPTION EXERCISE 
 Date:
[                        ] 
 Achillion Pharmaceuticals, Inc. 
 300 George Street 
 New Haven, CT 06511 
 Attention: Treasurer 
 Dear Sir
or Madam: 
 I am the holder of a Nonstatutory Stock Option granted to me under the Achillion Pharmaceuticals, Inc. (the “Company”)
2006 Stock Incentive Plan on [            ] for the purchase of [            ] shares of Common Stock of the Company at a
purchase price of [$            ] per share. 
 I hereby exercise my option to
purchase [            ] shares of Common Stock (the “Shares”), for which I have enclosed [            ]in the amount of
[            ]. Please register my stock certificate as follows: 
 Name(s):                                     
    
 Address:
                                        

 Tax I.D.
#:                                       

I represent, warrant and covenant as follows: 
 7. I am
purchasing the Shares for my own account for investment only, and not with a view to, or for sale in connection with, any distribution of the Shares in violation of the Securities Act of 1933 (the “Securities Act”), or any rule or
regulation under the Securities Act. 
 8. I have had such opportunity as I have deemed adequate to obtain from representatives of the Company such
information as is necessary to permit me to evaluate the merits and risks of my investment in the Company. 
 9. I have sufficient experience in business,
financial and investment matters to be able to evaluate the risks involved in the purchase of the Shares and to make an informed investment decision with respect to such purchase. 
 10. I can afford a complete loss of the value of the Shares and am able to bear the economic risk of holding such Shares for an indefinite period. 
  







 Exhibit A 
 11. I understand that (i) the Shares have not been registered under the Securities Act and are “restricted securities” within the meaning of Rule 144 under the Securities Act, (ii) the Shares
cannot be sold, transferred or otherwise disposed of unless they are subsequently registered under the Securities Act or an exemption from registration is then available; (iii) in any event, the exemption from registration under Rule 144 will
not be available for at least one year and even then will not be available unless a public market then exists for the Common Stock, adequate information concerning the Company is then available to the public, and other terms and conditions of Rule
144 are complied with; and (iv) there is now no registration statement on file with the Securities and Exchange Commission with respect to any stock of the Company and the Company has no obligation or current intention to register the Shares
under the Securities Act. 
 Very truly yours, 
 ____________________ 
 (Signature)