Sec Form 4 Filing - Clarus Lifesciences II, L.P. @ ACHILLION PHARMACEUTICALS INC - 2012-05-31

FORM 4 Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934, Section 17(a) of the Public Utility Holding Company Act of 1935 or Section 30(h) of the Investment Company Act of 1940

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1. Name and Address of Reporting Person Clarus Lifesciences II, L.P. 2. Issuer Name and Ticker or Trading Symbol ACHILLION PHARMACEUTICALS INC [ ACHN] 5. Relationship of Reporting Person(s) to Issuer (Check all applicable) _____ Director X __ 10% Owner _____ Officer (give title below) _____ Other (specify below) (Last) (First) (Middle) C/O CLARUS VENTURES, LLC, 101 MAIN STREET, SUITE 1210 3. Date of Earliest Transaction (MM/DD/YY) 05/31/2012 (Street) CAMBRIDGE, MA02142 4. If Amendment, Date Original Filed (MM/DD/YY) 6. Individual or Joint/Group Filing (Check Applicable Line) _____ Form filed by One Reporting Person __ X __ Form filed by More than One Reporting Person (City) (State) (Zip)

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned 1.Title of Security (Instr. 3) 2. Transaction Date (MM/DD/YY) 2A. Deemed Execution Date, if any (MM/DD/YY) 3. Transaction Code (Instr. 8) 4. Securities Acquired (A) or Disposed of (D) (Instr. 3, 4 and 5) 5. Amount of Securities Beneficially Owned Following Reported Transaction(s) (Instr. 3 and 4) 6. Ownership Form: Direct (D) or Indirect (I) (Instr. 4) 7. Nature of Indirect Beneficial Ownership (Instr. 4) Code V Amount (A) or (D) Price Common Stock 05/31/2012 X 1,290,922 A $ 3.53 10,553,001 I By Fund ( 1 ) Common Stock 05/31/2012 X 1,706,426 A $ 3.1125 12,259,427 I By Fund ( 1 ) Common Stock 05/31/2012 S( 2 ) 608,146 D $ 7.4932 11,651,281 I By Fund ( 1 ) Common Stock 05/31/2012 S( 3 ) 708,810 D $ 7.4932 10,942,471 I By Fund ( 1 )

Table II - Derivative Securities Acquired, Disposed of, or Beneficially Owned ( e.g. , puts, calls, warrants, options, convertible securities) 1. Title of Derivative Security (Instr. 3) 2. Conversion or Exercise Price of Derivative Security 3. Transaction Date (MM/DD/YY) 3A. Deemed Execution Date, if any (MM/DD/YY) 4. Transaction Code (Instr. 8) 5. Number of Derivative Securities Acquired (A) or Disposed of (D) (Instr. 3, 4, and 5) 6. Date Exercisable and Expiration Date (MM/DD/YY) 7. Title and Amount of Underlying Securities (Instr. 3 and 4) 8. Price of Derivative Security (Instr. 5) 9. Number of Derivative Securities Beneficially Owned Following Reported Tr ansaction(s) (Instr. 4) 10. Ownership Form of Derivative Security: Direct (D) or Indirect (I) (Instr. 4) 11. Nature of Indirect Beneficial Ownership (Instr. 4) Code V (A) (D) Date Exercisable Expiration Date Title Amount or Number of Shares Common Stock Warrant (right to buy) $ 3.1125 05/31/2012 X 1,706,426 08/20/2010 08/20/2017 Common Stock 1,706,426 $ 0 0 I By Fund ( 1 ) Common Stock Warrant (right to buy) $ 3.53 05/31/2012 X 1,290,922 08/12/2008 08/12/2015 Common Stock 1,290,922 $ 0 0 I By Fund ( 1 )

Reporting Owners Reporting Owner Name / Address Relationships Director 10% Owner Officer Other Clarus Lifesciences II, L.P. C/O CLARUS VENTURES, LLC 101 MAIN STREET, SUITE 1210 CAMBRIDGE, MA02142 X Clarus Ventures II GP, L.P. C/O CLARUS VENTURES, LLC 101 MAIN STREET, SUITE 1210 CAMBRIDGE, MA02142 X Clarus Ventures II, LLC C/O CLARUS VENTURES, LLC 101 MAIN STREET, SUITE 1210 CAMBRIDGE, MA02142 X LIPTAK ROBERT C/O CLARUS VENTURES, LLC 101 MAIN STREET, SUITE 1210 CAMBRIDGE, MA02142 X Simon Nicholas C/O CLARUS VENTURES, LLC 101 MAIN STREET, SUITE 1210 CAMBRIDGE, MA02142 X X HENNER DENNIS C/O CLARUS VENTURES, LLC 101 MAIN STREET, SUITE 1210 CAMBRIDGE, MA02142 X GALAKATOS NICHOLAS C/O CLARUS VENTURES, LLC 101 MAIN STREET, SUITE 1210 CAMBRIDGE, MA02142 X WHEELER KURT C/O CLARUS VENTURES, LLC 101 MAIN STREET, SUITE 1210 CAMBRIDGE, MA02142 X STEINMETZ MICHAEL C/O CLARUS VENTURES, LLC 101 MAIN STREET, SUITE 1210 CAMBRIDGE, MA02142 X Signatures /s/ Robert Liptak, Manager of Clarus Ventures II, LLC, general partner of Clarus Ventures II GP, L.P., general partner of Clarus Lifesciences II, L.P. 06/04/2012 Signature of Reporting Person Date /s/ Robert Liptak, Manager of Clarus Ventures II, LLC, general partner of Clarus Ventures II GP, L.P. 06/04/2012 Signature of Reporting Person Date /s/ Robert Liptak, Manager of Clarus Ventures II, LLC 06/04/2012 Signature of Reporting Person Date /s/ Robert Liptak, as attorney-in-fact for Nicholas Simon 06/04/2012 Signature of Reporting Person Date /s/ Robert Liptak 06/04/2012 Signature of Reporting Person Date /s/ Robert Liptak, as attorney-in-fact for Dennis Henner 06/04/2012 Signature of Reporting Person Date /s/ Robert Liptak, as attorney-in-fact for Nicholas Galakatos 06/04/2012 Signature of Reporting Person Date /s/ Robert Liptak, as attorney-in-fact for Kurt Wheeler 06/04/2012 Signature of Reporting Person Date /s/ Robert Liptak, as attorney-in-fact for Michael Steinmetz 06/04/2012 Signature of Reporting Person Date

Explanation of Responses:

( 1 )Securities held of record by Clarus Lifesciences II, L.P. (the "Fund"). Clarus Ventures II GP, L.P. (the "GPLP"), as the sole general partner of the Fund, may be deemed to beneficially own certain of the shares held of record by the Fund. The GPLP disclaims beneficial ownership of all shares held of record by the Fund in which the GPLP does not have an actual pecuniary interest. Clarus Ventures II, LLC (the "GPLLC"), as the sole general partner of the GPLP, may be deemed to beneficially own certain of the shares held of record by the Fund. Each of Messrs. Galakatos, Henner, Liptak, Simon, Steinmetz and Wheeler, as individual Managing Directors of the GPLLC, may be deemed to beneficially own certain of the shares held of record by the Fund. Each of the GPLLC and Messrs. Galakatos, Henner, Liptak, Simon, Steinmetz and Wheeler disclaims beneficial ownership of all shares held of record by the Fund in which he does not have an actual pecuniary interest. ( 2 )On May 31, 2012, the reporting person exercised warrants to purchase 1,290,922 shares of ACHN common stock for $3.53 a share. The reporting person paid the exercise price on a cashless basis, resulting in ACHN's withholding of 608,146 of the warrant shares to pay the exercise price and issuing the reporting person the remaining 682,776 shares. ( 3 )On May 31, 2012, the reporting person exercised warrants to purchase 1,706,426 shares of ACHN common stock for $3.1125 a share. The reporting person paid the exercise price on a cashless basis, resulting in ACHN's withholding of 708,810 of the warrant shares to pay the exercise price and issuing the reporting person the remaining 997,616 shares.

Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly.

* If the form is filed by more than one reporting person, see Instruction 4(b)(v).

** Intentional misstatements or omissions of facts constitute Federal Criminal Violations. See 18 U.S.C. 1001 and 15 U.S.C. 78ff(a).

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