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 OF SECURITIES
                                                                                  
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Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934 or Section 30(h) of the Investment Company Act of 1940
                      

1. Name and Address of Reporting Person *

RA CAPITAL MANAGEMENT, LLC
2. Issuer Name and Ticker or Trading Symbol

ACHILLION PHARMACEUTICALS INC [ ACHN ]
5. Relationship of Reporting Person(s) to Issuer (Check all applicable)

_____ Director                      _____ 10% Owner
_____ Officer (give title below)      __ X __ Other (specify below)
Former 10% Owner. See FN(1)(2)
(Last)          (First)          (Middle)

C/O RA CAPITAL MANAGEMENT, LLC, 20 PARK PLAZA, SUITE 1200
3. Date of Earliest Transaction (MM/DD/YYYY)

7/15/2013
(Street)

BOSTON, MA 02116
(City)        (State)        (Zip)
4. If Amendment, Date Original Filed (MM/DD/YYYY)

 
6. Individual or Joint/Group Filing (Check Applicable Line)

___ Form filed by One Reporting Person
_ X _ Form filed by More than One Reporting Person

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned
1.Title of Security
(Instr. 3)
2. Trans. Date 2A. Deemed Execution Date, if any 3. Trans. 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, $0.001 par value   9/16/2013     S    91801   D $7.5262   4867617   D   (1) (2)  
Common Stock, $0.001 par value   9/17/2013     S    77600   D $7.4226   4959418   D   (1) (2)  
Common Stock, $0.001 par value   9/18/2013     S    2328   D $7.4800   5037018   D   (1) (2)  
Common Stock, $0.001 par value   9/20/2013     S    26539   D $7.4035   5039346   D   (1) (2)  
Common Stock, $0.001 par value   9/23/2013     S    5665   D $7.4150   5065885   D   (1) (2)  
Common Stock, $0.001 par value   9/23/2013     S    27783   D $7.4192   5071550   D   (1) (2)  
Common Stock, $0.001 par value   9/24/2013     S    77600   D $7.3000   5099333   D   (1) (2)  
Common Stock, $0.001 par value   9/24/2013     S    4424   D $7.3300   5176933   D   (1) (2)  
Common Stock, $0.001 par value   9/24/2013     S    49354   D $7.3450   5181357   D   (1) (2)  
Common Stock, $0.001 par value   9/24/2013     S    50051   D $7.3800   5230711   D   (1) (2)  
Common Stock, $0.001 par value   9/25/2013     S    135800   D $7.2600   5280762   D   (1) (2)  
Common Stock, $0.001 par value   9/27/2013     P    200000   A $4.000   5416562   D   (1) (2)  
Common Stock, $0.001 par value   9/27/2013     P    400000   A $4.000   5216562   D   (1) (2)  
Common Stock, $0.001 par value   9/30/2013     P    1552000   A $3.500   4816562   D   (1) (2)  

Table II - Derivative Securities Beneficially Owned ( e.g. , puts, calls, warrants, options, convertible securities)
1. Title of Derivate Security
(Instr. 3)
2. Conversion or Exercise Price of Derivative Security 3. Trans. Date 3A. Deemed Execution Date, if any 4. Trans. 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 7. Title and Amount of Securities Underlying Derivative Security
(Instr. 3 and 4)
8. Price of Derivative Security
(Instr. 5)
9. Number of derivative Securities Beneficially Owned Following Reported Transaction(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

Explanation of Responses:
( 1)  The reported securities are owned by RA Capital Healthcare Fund, L.P. (the "Fund"). RA Capital Management, LLC (the "Adviser") is the general partner of the Fund, and Peter Kolchinsky is the sole manager of the Adviser. The Adviser and Mr. Kolchinsky disclaim beneficial ownership of the reported securities in reliance on Rule 16a-1(a)(1)(v) and (vii), respectively, and therefore disclaim any obligation to report ownership of the reported securities other than on behalf of the Fund. The filing of this Form 4 shall not be construed as an admission that either the Adviser or Mr. Kolchinsky is or was, for purposes of Section 16 of the Securities Exchange Act of 1934 or otherwise, the beneficial owner of any of the securities reported herein. The number of shares reported in Column 5 of Table I and the number of options reported in Column 9 of Table II reflect the number of shares or options, as applicable, beneficially owned by the Fund as of the filing date of this Form 4.
( 2)  On July 15, 2013, the Fund became a beneficial owner of more than ten percent of the outstanding shares the issuer's common stock and therefore became subject to Section 16 of the Securities Exchange Act of 1934. On September 23, 2014, the Fund ceased to be a beneficial owner of more than ten percent of the outstanding shares the issuer's common stock and ceased to be subject to Section 16.

Reporting Owners
Reporting Owner Name / Address
Relationships
Director 10% Owner Officer Other
RA CAPITAL MANAGEMENT, LLC
C/O RA CAPITAL MANAGEMENT, LLC
20 PARK PLAZA, SUITE 1200
BOSTON, MA 02116



Former 10% Owner. See FN(1)(2)
RA Capital Healthcare Fund LP
C/O RA CAPITAL MANAGEMENT, LLC
20 PARK PLAZA, SUITE 1200
BOSTON, MA 02116

X

Kolchinsky Peter
C/O RA CAPITAL MANAGEMENT, LLC
20 PARK PLAZA, SUITE 1200
BOSTON, MA 02116

X


Signatures
/s/ Peter Kolchinsky, Manager of RA Capital Management, LLC 1/20/2015
** Signature of Reporting Person Date

/s/ Peter Kolchinsky, individually 1/20/2015
** Signature of Reporting Person Date

/s/ Peter Kolchinsky, Manager of RA Capital Management, LLC, the General Partner of RA Capital Healthcare Fund, L.P. 1/20/2015
** Signature of Reporting Person Date


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).
Note: File three copies of this Form, one of which must be manually signed. If space is insufficient, see Instruction 6 for procedure.
Persons who respond to the collection of information contained in this form are not required to respond unless the form displays a currently valid OMB control number.
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