SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549
Schedule 13G
(Rule 13d-102)
INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1 (b),
(c) AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO 13d-2 (b)
(Amendment No. 3)*
Alnylam Pharmaceuticals, Inc.
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(Name of Issuer)
Common Stock
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(Title of Class of Securities)
02043Q107
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(CUSIP Number)
December 30, 2005
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(Date of Event Which Requires Filing of this Statement)
Check the appropriate box to designate the rule pursuant to which this Schedule
is filed:
Rule 13d-1(b)
Rule 13d-1(c)
X Rule 13d-1(d)
*The remainder of this cover page shall be filled out for a reporting person's
initial filing on this form with respect to the subject class of securities, and
for any subsequent amendment containing information which would alter
disclosures provided in a prior cover page.
The information required on the remainder of this cover page shall not be deemed
to be "filed" for the purpose of Section 18 of the Securities Exchange Act of
1934 ("Act") or otherwise subject to the liabilities of that section of the Act
but shall be subject to all other provisions of the Act (however, see the
Notes).
(Continued on following pages)
Page 1 of 16
Exhibit Index on Page 13
CUSIP NO. 02043Q107 13 G Page 2 of 16
1 NAME OF REPORTING
SS OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
Polaris Venture Partners III, L.P. ("PVP III")
2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
(a) (b) X
3 SEC USE ONLY
4 CITIZENSHIP OR PLACE OF ORGANIZATION
Delaware
5 SOLE VOTING POWER
NUMBER OF 365,852 shares, except that Polaris Venture
SHARES Management Co. III, L.L.C. ("Polaris III"), the
BENEFICIALLY general partner of PVP III, may be deemed to
OWNED BY EACH REPORTING have sole power to vote these shares, and
PERSON Jonathan A. Flint ("Flint"), Terrance G. McGuire
WITH ("McGuire") and Alan G. Spoon ("Spoon"), the
managing members of Polaris III, may be deemed to
have shared power to vote these shares.
6 SHARED VOTING POWER
See response to row 5.
7 SOLE DISPOSITIVE POWER
365,852 shares, except that Polaris III, the
general partner of PVP III, may be deemed to have
sole power to dispose of these shares, and Flint,
McGuire and Spoon, the managing members of
Polaris III, may be deemed to have shared power
to dispose of these shares.
8 SHARED DISPOSITIVE POWER
See response to row 7.
9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH
REPORTING PERSON 365,852
10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9)
EXCLUDES CERTAIN SHARES
11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
1.37%
12 TYPE OF REPORTING PERSON
PN
CUSIP NO. 02043Q107 13 G Page 3 of 16
1 NAME OF REPORTING
SS OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
Polaris Venture Partners Entrepreneurs' Fund III, L.P.
("Entrepreneurs' III")
2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
(a) (b) X
3 SEC USE ONLY
4 CITIZENSHIP OR PLACE OF ORGANIZATION
Delaware
5 SOLE VOTING POWER
NUMBER OF 9,372 shares, except that Polaris III, the
SHARES general partner of Entrepreneurs' III, may be
BENEFICIALLY deemed to have sole power to vote these shares,
OWNED BY EACH REPORTING and Flint, McGuire and Spoon, the managing
PERSON members of Polaris III, may be deemed to have
WITH shared power to vote these shares.
6 SHARED VOTING POWER
See response to row 5.
7 SOLE DISPOSITIVE POWER
9,372 shares, except that Polaris III, the
general partner of Entrepreneurs' III, may be
deemed to have sole power to dispose of these
shares, and Flint, McGuire and Spoon, the
managing members of Polaris III, may be deemed to
have shared power to dispose of these shares.
8 SHARED DISPOSITIVE POWER
See response to row 7.
9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH
REPORTING PERSON 9,372
10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9)
EXCLUDES CERTAIN SHARES
11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
0.04%
12 TYPE OF REPORTING PERSON
PN
CUSIP NO. 02043Q107 13 G Page 4 of 16
1 NAME OF REPORTING
SS OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
Polaris Venture Partners Founders' Fund III, L.P. ("Founders' III")
2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
(a) (b) X
3 SEC USE ONLY
4 CITIZENSHIP OR PLACE OF ORGANIZATION
Delaware
5 SOLE VOTING POWER
NUMBER OF 5,701 shares, except that Polaris III, the
SHARES general partner of Founders' III, may be deemed
BENEFICIALLY to have sole power to vote these shares, and
OWNED BY EACH REPORTING Flint, McGuire and Spoon, the managing members
PERSON of Polaris III, may be deemed to have shared
WITH power to vote these shares.
6 SHARED VOTING POWER
See response to row 5.
7 SOLE DISPOSITIVE POWER
5,701 shares, except that Polaris III, the
general partner of Founders' III, may be deemed
to have sole power to dispose of these shares,
and Flint, McGuire and Spoon, the managing
members of Polaris III, may be deemed to have
shared power to dispose of these shares.
8 SHARED DISPOSITIVE POWER
See response to row 7.
9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH
REPORTING PERSON 5,701
10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9)
EXCLUDES CERTAIN SHARES
11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
0.02%
12 TYPE OF REPORTING PERSON
PN
CUSIP NO. 02043Q107 13 G Page 5 of 16
1 NAME OF REPORTING
SS OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
Polaris Venture Management Co. III, L.L.C. ("Polaris III")
2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
(a) (b) X
3 SEC USE ONLY
4 CITIZENSHIP OR PLACE OF ORGANIZATION
Delaware
5 SOLE VOTING POWER
NUMBER OF 380,925 shares, of which 365,852 are directly
SHARES owned by PVP III, 9,372 are directly owned by
BENEFICIALLY Entrepreneurs' III and 5,701 are directly owned
OWNED BY EACH REPORTING by Founders' III. Polaris III, the general
PERSON partner of PVP III, Entrepreneurs' III and
WITH Founders' III, may be deemed to have sole power
to vote these shares, and Flint, McGuire and
Spoon, the managing members of Polaris III, may
be deemed to have shared power to vote these
shares.
6 SHARED VOTING POWER
See response to row 5.
7 SOLE DISPOSITIVE POWER
380,925 shares, of which 365,852 are directly
owned by PVP III, 9,372 are directly owned by
Entrepreneurs' III and 5,701 are directly owned
by Founders' III. Polaris III, the general
partner of PVP III, Entrepreneurs' III and
Founders' III, may be deemed to have sole power
to vote these shares, and Flint, McGuire and
Spoon, the managing members of Polaris III, may
be deemed to have shared power to dispose of
these shares.
8 SHARED DISPOSITIVE POWER
See response to row 7.
9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH
REPORTING PERSON 380,925
10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9)
EXCLUDES CERTAIN SHARES
11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
1.43%
12 TYPE OF REPORTING PERSON
OO
CUSIP NO. 02043Q107 13 G Page 6 of 16
1 NAME OF REPORTING
SS OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
Jonathan A. Flint ("Flint")
2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
(a) (b) X
3 SEC USE ONLY
4 CITIZENSHIP OR PLACE OF ORGANIZATION
U.S. Citizen
5 SOLE VOTING POWER
0 shares.
NUMBER OF
SHARES
BENEFICIALLY 6 SHARED VOTING POWER
OWNED BY EACH REPORTING 380,925 shares, of which 365,852 are directly
PERSON owned by PVP III, 9,372 are directly owned by
WITH Entrepreneurs' III and 5,701 are directly owned
by Founders' III. Polaris III is the general
partner of PVP III, Entrepreneurs' III and
Founders' III. Flint is a managing member of
Polaris III, and may be deemed to have shared
power to vote these shares.
7 SOLE DISPOSITIVE POWER
0 shares.
8 SHARED DISPOSITIVE POWER
380,925 shares, of which 365,852 are directly
owned by PVP III, 9,372 are directly owned by
Entrepreneurs' III and 5,701 are directly owned
by Founders' III. Polaris III is the general
partner of PVP III, Entrepreneurs' III and
Founders' III. Flint is a managing member of
Polaris III, and may be deemed to have shared
power to dispose of these shares.
9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH
REPORTING PERSON 380,925
10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9)
EXCLUDES CERTAIN SHARES
11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
1.43%
12 TYPE OF REPORTING PERSON
IN
CUSIP NO. 02043Q107 13 G Page 7 of 16
1 NAME OF REPORTING
SS OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
Terrance G. McGuire ("McGuire")
2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
(a) (b) X
3 SEC USE ONLY
4 CITIZENSHIP OR PLACE OF ORGANIZATION
U.S. Citizen
5 SOLE VOTING POWER
0 shares.
NUMBER OF
SHARES
BENEFICIALLY 6 SHARED VOTING POWER
OWNED BY EACH REPORTING 380,925 shares, of which 365,852 are directly
PERSON owned by PVP III, 9,372 are directly owned by
WITH Entrepreneurs' III and 5,701 are directly owned
by Founders' III. Polaris III is the general
partner of PVP III, Entrepreneurs' III and
Founders' III. McGuire is a managing member of
Polaris III, and may be deemed to have shared
power to vote these shares.
7 SOLE DISPOSITIVE POWER
0 shares.
8 SHARED DISPOSITIVE POWER
380,925 shares, of which 365,852 are directly
owned by PVP III, 9,372 are directly owned by
Entrepreneurs' III and 5,701 are directly owned
by Founders' III. Polaris III is the general
partner of PVP III, Entrepreneurs' III and
Founders' III. McGuire is a managing member of
Polaris III, and may be deemed to have shared
power to dispose of these shares.
9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH
REPORTING PERSON 380,925
10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9)
EXCLUDES CERTAIN SHARES
11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
1.43%
12 TYPE OF REPORTING PERSON
IN
CUSIP NO. 02043Q107 13 G Page 8 of 16
1 NAME OF REPORTING
SS OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
Alan G. Spoon ("Spoon")
2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
(a) (b) X
3 SEC USE ONLY
4 CITIZENSHIP OR PLACE OF ORGANIZATION
U.S. Citizen
5 SOLE VOTING POWER
0 shares.
NUMBER OF
SHARES
BENEFICIALLY 6 SHARED VOTING POWER
OWNED BY EACH REPORTING 380,925 shares, of which 365,852 are directly
PERSON owned by PVP III, 9,372 are directly owned by
WITH Entrepreneurs' III and 5,701 are directly owned
by Founders' III. Polaris III is the general
partner of PVP III, Entrepreneurs' III and
Founders' III. Spoon is a managing member of
Polaris III, and may be deemed to have shared
power to vote these shares.
7 SOLE DISPOSITIVE POWER
0 shares.
8 SHARED DISPOSITIVE POWER
380,925 shares, of which 365,852 are directly
owned by PVP III, 9,372 are directly owned by
Entrepreneurs' III and 5,701 are directly owned
by Founders' III. Polaris III is the general
partner of PVP III, Entrepreneurs' III and
Founders' III. Spoon is a managing member of
Polaris III, and may be deemed to have shared
power to dispose of these shares.
9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH
REPORTING PERSON 380,925
10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9)
EXCLUDES CERTAIN SHARES
11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
1.43%
12 TYPE OF REPORTING PERSON
IN
CUSIP NO. 02043Q107 13 G Page 9 of 16
ITEM 1(A). NAME OF ISSUER
Alnylam Pharmaceuticals, Inc.
ITEM 1(B). ADDRESS OF ISSUER'S PRINCIPAL EXECUTIVE OFFICES
300 Third Street
Cambridge, Massachusetts 02142
ITEM 2(A). NAME OF PERSONS FILING
This Statement is filed by Polaris Venture Partners III, L.P.,
a Delaware limited partnership ("PVP III"), Polaris Venture
Partners Entrepreneurs' Fund III, L.P., a Delaware limited
partnership ("Entrepreneurs' III"), Polaris Venture Partners
Founders' Fund III, L.P., a Delaware limited partnership
("Founders' III"), Polaris Venture Management Co. III, L.L.C.,
a Delaware limited liability company ("Polaris III"), Jonathan
A. Flint ("Flint"), Terrance G. McGuire ("McGuire") and Alan
G. Spoon ("Spoon"). Flint, McGuire and Spoon are the managing
members of Polaris III. The foregoing entities and individuals
are collectively referred to as the "Reporting Persons."
Polaris III, the general partner of PVP III, Entrepreneurs'
III and Founders' III, may be deemed to have sole power to
vote and sole power to dispose of shares of the issuer
directly owned by PVP III, Entrepreneurs' III and Founders'
III. Flint, McGuire and Spoon are the managing members of
Polaris III and may be deemed to have shared power to vote and
shared power to dispose of shares of the issuer directly owned
by PVP III, Entrepreneurs' III and Founders' III.
ITEM 2(B). ADDRESS OF PRINCIPAL OFFICE
The address for each of the Reporting Persons is:
Polaris Venture Partners
1000 Winter Street, Suite 3350
Waltham, Massachusetts 02451
ITEM 2(C) CITIZENSHIP
PVP III, Entrepreneurs' III and Founders' III are Delaware
limited partnerships; Polaris III is a Delaware Limited
Liability Company; Flint, McGuire and Spoon are United States
citizens.
ITEM 2(D) AND (E). TITLE OF CLASS OF SECURITIES AND CUSIP NUMBER
Common Stock
CUSIP # 02043Q107
ITEM 3. Not Applicable
ITEM 4. OWNERSHIP
The following information with respect to the ownership of the
Common Stock of the issuer by the persons filing this
Statement is provided as of December 30, 2005:
(a) Amount beneficially owned:
See Row 9 of cover page for each Reporting
Person.
(b) Percent of Class:
CUSIP NO. 02043Q107 13 G Page 10 of 16
See Row 11 of cover page for each Reporting
Person.
(c) Number of shares as to which such person has:
(i) Sole power to vote or to direct
the vote:
See Row 5 of cover page for
each Reporting Person.
(ii) Shared power to vote or to direct
the vote:
See Row 6 of cover page for
each Reporting Person.
(iii) Sole power to dispose or to
direct the disposition of:
See Row 7 of cover page for
each Reporting Person.
(iv) Shared power to dispose or to
direct the disposition of:
See Row 8 of cover page for
each Reporting Person.
ITEM 5. OWNERSHIP OF FIVE PERCENT OR LESS OF A CLASS.
Not applicable.
ITEM 6. OWNERSHIP OF MORE THAN FIVE PERCENT ON BEHALF OF ANOTHER
PERSON.
Under certain circumstances set forth in the limited
partnership agreements of PVP III, Entrepreneurs' III and
Founders' III, the general and limited partners of each of
such entities may be deemed to have the right to receive
dividends from, or the proceeds from, the sale of shares of
the issuer owned by each such entity of which they are a
partner.
ITEM 7. IDENTIFICATION AND CLASSIFICATION OF THE SUBSIDIARY WHICH
ACQUIRED THE SECURITY BEING REPORTED ON BY THE PARENT HOLDING
COMPANY
Not applicable.
ITEM 8. IDENTIFICATION AND CLASSIFICATION OF MEMBERS OF THE GROUP.
Not applicable.
ITEM 9. NOTICE OF DISSOLUTION OF GROUP.
Not applicable.
ITEM 10. CERTIFICATION.
Not applicable.
Page 11 of 16
SIGNATURES
After reasonable inquiry and to the best of my knowledge and
belief, I certify that the information set forth in this statement is true,
complete and correct.
Dated: February 22, 2006
POLARIS VENTURE PARTNERS III, L.P., /s/ Kevin Littlejohn
a Delaware Limited Partnership -----------------------------------
Signature
Kevin Littlejohn
Authorized Signatory
POLARIS VENTURE PARTNERS /s/ Kevin Littlejohn
ENTREPRENEURS' FUND III, L.P., ------------------------------------
a Delaware Limited Partnership Signature
Kevin Littlejohn
Authorized Signatory
POLARIS VENTURE PARTNERS /s/ Kevin Littlejohn
FOUNDERS' FUND III, L.P., ------------------------------------
a Delaware Limited Partnership Signature
Kevin Littlejohn
Authorized Signatory
POLARIS VENTURE
MANAGEMENT CO. III, L.L.C., /s/ Kevin Littlejohn
a Delaware Limited Liability Company ------------------------------------
Signature
Kevin Littlejohn
Authorized Signatory
JONATHAN A. FLINT /s/ Kevin Littlejohn
------------------------------------
Signature
Kevin Littlejohn
Authorized Signatory
Page 12 of 16
TERRANCE G. MCGUIRE /s/ Kevin Littlejohn
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Signature
Kevin Littlejohn
Authorized Signatory
ALAN G. SPOON /s/ Kevin Littlejohn
------------------------------------
Signature
Kevin Littlejohn
Authorized Signatory
Page 13 of 16
EXHIBIT INDEX
Found on
Sequentially
Exhibit Numbered Page
------- -------------
Exhibit A: Agreement of Joint Filing 14
Exhibit B: Reference to Kevin Littlejohn as Authorized Signatory 16
Page 14 of 16
EXHIBIT A
Agreement of Joint Filing
The undersigned hereby agree that a single Schedule 13G (or
any amendment thereto) relating to the Common Stock of Alnylam Pharmaceuticals,
Inc. shall be filed on behalf of each of the undersigned and that this Agreement
shall be filed as an exhibit to such Schedule 13G.
Dated: February 22, 2006
POLARIS VENTURE PARTNERS III, L.P., /s/ Kevin Littlejohn
a Delaware Limited Partnership ------------------------------------
Signature
Kevin Littlejohn
Authorized Signatory
POLARIS VENTURE PARTNERS /s/ Kevin Littlejohn
ENTREPRENEURS' FUND III, L.P., ------------------------------------
a Delaware Limited Partnership Signature
Kevin Littlejohn
Authorized Signatory
POLARIS VENTURE PARTNERS /s/ Kevin Littlejohn
FOUNDERS' FUND III, L.P., ------------------------------------
a Delaware Limited Partnership Signature
Kevin Littlejohn
Authorized Signatory
POLARIS VENTURE
MANAGEMENT CO. III, L.L.C., /s/ Kevin Littlejohn
a Delaware Limited Liability Company ------------------------------------
Signature
Kevin Littlejohn
Authorized Signatory
JONATHAN A. FLINT /s/ Kevin Littlejohn
------------------------------------
Signature
Kevin Littlejohn
Authorized Signatory
Page 15 of 16
TERRANCE G. MCGUIRE /s/ Kevin Littlejohn
------------------------------------
Signature
Kevin Littlejohn
Authorized Signatory
ALAN G. SPOON /s/ Kevin Littlejohn
------------------------------------
Signature
Kevin Littlejohn
Authorized Signatory
Page 16 of 16
EXHIBIT B
REFERENCE TO KEVIN LITTLEJOHN AS AUTHORIZED SIGNATORY
Kevin Littlejohn has signed the enclosed documents as Authorized Signatory. Note
that copies of the applicable Agreement to File Jointly and Statement Appointing
Designated Filer and Authorized Signatory are already on file with the
appropriate agencies.