SCHEDULE
13G
SECURITIES
AND EXCHANGE COMMISSION
WASHINGTON,
DC 20549
Under the
Securities Exchange Act of 1934
(Amendment
No. 1)*
PHARMATHENE,
INC.
Common
Stock, par value $0.0001 per share
(Title of
Class of Securities)
71714G102
(CUSIP Number)
December
31, 2009
(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)
x Rule
13d-1(c)
¨ 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 (the “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).
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CUSIP No. 71714G102
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1
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NAMES
OF REPORTING PERSONS
I.R.S.
IDENTIFICATION NOS. OF ABOVE PERSONS (entities only)
Felix J.
Baker
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2
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CHECK
THE APPROPRIATE BOX IF A MEMBER OF A GROUP (See
Instructions) (a)
¨
(b)
¨
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3
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SEC
USE ONLY
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4
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CITIZENSHIP
OR PLACE OF ORGANIZATION
United
States
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NUMBER
OF
SHARES
BENEFICIALLY
OWNED
BY
EACH
REPORTING
PERSON
WITH
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5
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SOLE
VOTING POWER
-0-
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6
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SHARED
VOTING POWER
2,843,557
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7
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SOLE
DISPOSITIVE POWER
-0-
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8
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SHARED
DISPOSITIVE POWER
2,843,557
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9
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AGGREGATE
AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
2,843,557
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10
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CHECK BOX IF THE AGGREGATE
AMOUNT IN ROW (9) EXCLUDES CERTAIN
SHARES ¨
(See
Instructions)
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11
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PERCENT
OF CLASS REPRESENTED BY AMOUNT IN ROW 9
9.9%
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12
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TYPE
OF REPORTING PERSON (See Instructions)
IN
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Page 2 of
8 Pages
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CUSIP No. 71714G102
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1
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NAMES
OF REPORTING PERSONS
I.R.S.
IDENTIFICATION NOS. OF ABOVE PERSONS (entities only)
Julian C.
Baker
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2
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CHECK
THE APPROPRIATE BOX IF A MEMBER OF A GROUP (See
Instructions)
(a) ¨
(b) ¨
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3
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SEC
USE ONLY
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4
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CITIZENSHIP
OR PLACE OF ORGANIZATION
United
States
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NUMBER
OF
SHARES
BENEFICIALLY
OWNED
BY
EACH
REPORTING
PERSON
WITH
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5
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SOLE
VOTING POWER
-0-
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6
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SHARED
VOTING POWER
2,843,557
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||
|
7
|
SOLE
DISPOSITIVE POWER
-0-
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||
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8
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SHARED
DISPOSITIVE POWER
2,843,557
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||
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9
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AGGREGATE
AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
2,843,557
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||
|
10
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CHECK BOX IF THE AGGREGATE
AMOUNT IN ROW (9) EXCLUDES CERTAIN
SHARES ¨
(See
Instructions)
|
||
|
11
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PERCENT
OF CLASS REPRESENTED BY AMOUNT IN ROW 9
9.9%
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12
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TYPE
OF REPORTING PERSON (See Instructions)
IN
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Page 3 of
8 Pages
Item
1(a) Name
of Issuer:
Pharmathene,
Inc.
Item
1(b) Address
of Issuer’s Principal Executive Offices:
One Park
Place, Ste. 450
Annapolis,
MD 21401
Item
2(a) Name
of Person Filing:
This
Schedule 13G is being filed jointly by Felix J. Baker and Julian C. Baker (the
“Reporting Persons”).
Item
2(b) Address
of Principal Business Office or, if None, Residence:
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Name
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Business Address
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Felix
J. Baker
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667
Madison Avenue
New
York, NY 10065
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Julian
C. Baker
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667
Madison Avenue
New
York,
NY 10065
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Item
2(c) Citizenship:
Each of the Reporting Persons is a
United States citizen.
Item
2(d) Title
of Class of Securities:
Common Stock, par value $0.001 per
share
Item
2(e) CUSIP
Number:
71714G102
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Item
3.
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If
this statement is filed pursuant to §§240.13d-1(b) or (c), check whether
the person filing is
a: N/A
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(a) ¨ Broker
or dealer registered under Section 15 of the Exchange Act.
(b) ¨ Bank
as defined in section 3(a)(6) of the Exchange Act.
(c) ¨
Insurance company as defined in section 3(a)(19) of the Exchange
Act.
(d) ¨
Investment company registered under section 8 of the Investment Company Act of
1940.
(e) ¨ An
investment adviser in accordance with Rule 13d-1(b)(1)(ii)(E).
Page 4 of
8 Pages
(f) ¨ An
employee benefit plan or endowment fund in accordance with Rule
13d-1(b)(1)(ii)(F).
(g) ¨ A
parent holding company or control person in accordance with Rule
13d-1(b)(1)(ii)(G).
(h) ¨ A
savings association as defined in Section 3(b) of the Federal Deposit Insurance
Act.
(i) ¨ A
church plan that is excluded from the definition of an investment company under
section 3(c)(14) of the Investment Company Act of 1940.
(j) ¨ Group,
in accordance with Rule 13d-1(b)(1)(ii)(J).
Item
4. Ownership.
Set forth below is the aggregate number
of shares of Common Stock held, including shares that may be acquired upon
conversion of Convertible notes due July 28, 2011 up to 9.999% of outstanding
shares and shares that may be acquired upon the exercise of Warrants, as of the
date hereof by each of the following, together with the percentage of
outstanding shares of Common Stock that such number represents based upon
28,435,598 shares outstanding to information obtained from the Company on
November 13, 2009 and the number of shares of common stock that would have been
issued upon conversion of the convertible notes if converted and the warrants if
exercised.
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Name
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Number of
Shares
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Percent of Class
Outstanding
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Baker
Bros. Investments II, L.P.
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3,375 | 0.0 | % | |||||
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667,
L.P.
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4,631 | 0.0 | % | |||||
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Baker
Brothers Life Sciences, L.P.
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2,843,557 | 9.9 | % | |||||
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14159,
L.P.
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107,675 | 0.4 | % | |||||
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Baker/Tisch
Investments, L.P.
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638 | 0.0 | % | |||||
The 10% convertible notes are only
convertible to the extent that the holders thereof and their affiliates would
beneficially own, for purposes of Section 13(d) of the Securities Exchange Act
of 1934, as amended, no more than 9.999% of the outstanding shares of Common
Stock of the Issuer after conversion. As a result of this restriction, the
number of shares that may be issued on conversion of the notes by the above
holders may change depending upon changes in the outstanding
shares. The number of shares issuable upon conversion of the notes
held by any particular Baker Bros. affiliate will also depend upon the extent to
which the notes held by other Baker Bros. affiliates have theretofore been
converted.
Page 5 of
8 Pages
By virtue of their ownership of
entities that have the power to control the investment decisions of the limited
partnerships listed in the table above, Felix J. Baker and Julian C. Baker may
each be deemed to be beneficial owners of shares owned by such entities and may
be deemed to have shared power to vote or direct the vote of and shared power to
dispose or direct the disposition of such securities.
Item
5. Ownership
of Five Percent or Less of a Class.
If this statement is being filed to
report the fact that as of the date hereof the reporting person has ceased to be
the beneficial owner of more than five percent of the class of securities, check
the following ¨. N/A
Item
6. Ownership
of More than Five Percent on Behalf of Another Person.
The
entities listed in Item 4 above are investment funds the investors in which have
the right to receive dividends, interest and the proceeds of sale of securities
owned by such funds.
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Item
7.
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Identification
and Classification of the Subsidiary Which Acquired the Security Being
Reported on by the Parent Holding Company or Control
Person.
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N/A
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Item
8.
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Identification
and Classification of Members of the
Group.
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N/A
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Item
9.
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Notice
of Dissolution of Group.
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N/A
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Item
10.
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Certification.
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By signing below I certify that, to the
best of my knowledge and belief, the securities referred to above were not
acquired and are not held for the purpose of or with the effect of changing or
influencing the control of the issuer of the securities and were not acquired
and are not held in connection with or as a participant in any transaction
having that purpose or effect.
Page 6 of
8 Pages
SIGNATURE
After reasonable inquiry and to the
best of my knowledge and belief, I hereby certify that the information set forth
in this statement is true, complete and correct.
February
16, 2010
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/s/
Felix J. Baker
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Felix
J. Baker
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/s/
Julian C. Baker
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Julian
C. Baker
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Page 7 of
8 Pages
AGREEMENT
In accordance with
Rule 13d-1(k)(1) under the Securities Exchange Act of 1934, as amended, the
undersigned hereby agree that this Statement on Schedule 13G relating to
the Common Stock of Pharmathene, Inc. is being filed with the Securities and
Exchange Commission on behalf of each of them.
February
16, 2010
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/s/
Felix J. Baker
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Felix
J. Baker
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/s/
Julian C. Baker
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Julian
C. Baker
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Page 8 of
8 Pages