FORM 3
        
UNITED STATES SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

INITIAL STATEMENT OF 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. Date of Event Requiring Statement (MM/DD/YYYY)
7/15/2013 

3. Issuer Name and Ticker or Trading Symbol

ACHILLION PHARMACEUTICALS INC [ACHN]

(Last)        (First)        (Middle)

C/O RA CAPITAL MANAGEMENT, LLC, 20 PARK PLAZA, SUITE 1200

4. Relationship of Reporting Person(s) to Issuer (Check all applicable)

_____ Director                            ___ X ___ 10% Owner
_____ Officer (give title below)          _____ Other (specify below)

(Street)

BOSTON, MA 02116       

(City)              (State)              (Zip)
5. If Amendment, Date Original Filed (MM/DD/YYYY)

10/4/2013 

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 Beneficially Owned
1.Title of Security
(Instr. 4)
2. Amount of Securities Beneficially Owned
(Instr. 4)
3. Ownership Form: Direct (D) or Indirect (I)
(Instr. 5)
4. Nature of Indirect Beneficial Ownership
(Instr. 5)
Common Stock, $0.001 par value   6842944   D   (1) (2)  

Table II - Derivative Securities Beneficially Owned ( e.g. , puts, calls, warrants, options, convertible securities)
1. Title of Derivate Security
(Instr. 4)
2. Date Exercisable and Expiration Date
(MM/DD/YYYY)
3. Title and Amount of Securities Underlying Derivative Security
(Instr. 4)
4. Conversion or Exercise Price of Derivative Security 5. Ownership Form of Derivative Security: Direct (D) or Indirect (I)
(Instr. 5)
6. Nature of Indirect Beneficial Ownership
(Instr. 5)
Date Exercisable Expiration Date Title Amount or Number of Shares
Call Option (right to buy)     (3) 1/18/2014   Common Stock   743500   (4) $10.00   D   (1) (2)  
Call Option (obligation to sell)     (3) 1/18/2014   Common Stock   743500   (4) $20.00   D   (1) (2)  
Call Option (right to buy)     (3) 1/18/2014   Common Stock   745000   (5) $10.00   D   (1) (2)  
Call Option (obligation to sell)     (3) 1/18/2014   Common Stock   745000   (5) $20.00   D   (1) (2)  
Call Option (right to buy)     (3) 1/17/2015   Common Stock   384000   (6) $7.50   D   (1) (2)  
Call Option (obligation to sell)     (3) 1/17/2015   Common Stock   384000   (6) $20.00   D   (1) (2)  
Call Option (right to buy)     (3) 1/17/2015   Common Stock   384000   (6) $7.50   D   (1) (2)  
Call Option (obligation to sell)     (3) 1/17/2015   Common Stock   384000   (6) $20.00   D   (1) (2)  
Call Option (right to buy)     (3) 1/17/2015   Common Stock   768000   (7) $7.50   D   (1) (2)  
Call Option (obligation to sell)     (3) 1/17/2015   Common Stock   768000   (7) $20.00   D   (1) (2)  

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 3/A 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.
( 2)  This amendment is being filed to report the Fund's holdings as of July 15, 2013, the date on which the Fund became the beneficial owner of more than 10% of the issuer's outstanding common stock. This amendment reports all equity securities of the issuer beneficially owned by the Fund as of the time the Fund became subject to Section 16.
( 3)  These options are exercisable at any time prior to their expiration.
( 4)  These options reflect an "option spread" strategy pursuant to which the Fund simultaneously (1) purchased 7,435 call option contracts, each representing a right to purchase 100 shares of the issuer's common stock at $10.00 per share and (2) sold 7,435 call option contracts, each representing an obligation to sell 100 shares of the issuer's common stock at $20.00 per share.
( 5)  These options reflect an "option spread" strategy pursuant to which the Fund simultaneously (1) purchased 7,450 call option contracts, each representing a right to purchase 100 shares of the issuer's common stock at $10.00 per share and (2) sold 7,450 call option contracts, each representing an obligation to sell 100 shares of the issuer's common stock at $20.00 per share.
( 6)  These options reflect an "option spread" strategy pursuant to which the Fund simultaneously (1) purchased 3,840 call option contracts, each representing a right to purchase 100 shares of the issuer's common stock at $7.50 per share and (2) sold 3,840 call option contracts, each representing an obligation to sell 100 shares of the issuer's common stock at $20.00 per share.
( 7)  These options reflect an "option spread" strategy pursuant to which the Fund simultaneously (1) purchased 7,680 call option contracts, each representing a right to purchase 100 shares of the issuer's common stock at $7.50 per share and (2) sold 7,680 call option contracts, each representing an obligation to sell 100 shares of the issuer's common stock at $20.00 per share.

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

X

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 5(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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