Check the appropriate box to designate the rule pursuant to
which this Schedule is filed:
*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 the disclosures provided in a prior cover page.
The information required in 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).
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1.
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Names
of Reporting Persons.
I.R.S. Identification Nos. of above persons (entities only).
RA
Capital Management, L.P.
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2.
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Check
the Appropriate Box if a Member of a Group (See Instructions)
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(a)
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¨
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(b)
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¨
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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 Delaware
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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
shares
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6.
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Shared
Voting Power 1,648,4851
shares
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7.
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Sole
Dispositive Power 0
shares
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8.
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Shared
Dispositive Power 1,648,4851
shares
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9.
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Aggregate
Amount Beneficially Owned by Each Reporting Person
1,648,4851 shares
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10.
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Check
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%2
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12.
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Type
of Reporting Person (See Instructions)
IA,
PN
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1
The shares reported herein for the Reporting Person represent (i) 270,292 shares of the Issuer’s Common Stock beneficially
owned (ii) 1,057,000 shares of the Issuer’s Common Stock the Reporting Person has the right to acquire through the exercise
of pre-funded warrants (“Pre-Funded Warrants”) and (iii) 1,136,000 shares of the Issuer’s Common Stock the Reporting
Person has the right to acquire through the exercise of Class A Warrants (“Class A Warrants”). The Pre-Funded Warrants
and the Class A Warrants contain a provision (the “Beneficial Ownership Blocker”) which precludes exercise of the warrants
to the extent that, following exercise, the Reporting Person, together with its affiliates and other attribution parties, would
own more than 9.99% of the Common Stock Outstanding. As a result, the Reporting Person is currently prohibited from exercising
the warrants to the extent that exercise would result in ownership of more than 1,648,485 shares of Common Stock.
2 The number
of shares outstanding for purposes of this percentage calculation assumes (i) 16,102,872 outstanding shares of Common Stock of
the Issuer, based on the Issuer’s Form 424B5 Prospectus as filed with the Securities and Exchange Commission (“SEC”)
on November 27, 2019, plus (ii) 398,485 shares of Common Stock of which the Reporting Person may acquire beneficial ownership
upon the exercise of Pre-Funded Warrants and Class A Warrants, as limited by the Beneficial Ownership Blocker.
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1.
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Names
of Reporting Persons.
I.R.S. Identification Nos. of above persons (entities only).
Peter
Kolchinsky
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2.
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Check
the Appropriate Box if a Member of a Group (See Instructions)
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(a)
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¨
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(b)
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¨
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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
shares
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|
|
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6.
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Shared
Voting Power 1,648,4851
shares
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7.
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Sole
Dispositive Power 0
shares
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8.
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Shared
Dispositive
Power 1,648,4851
shares
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9.
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Aggregate
Amount Beneficially Owned by Each Reporting Person
1,648,4851
shares
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10.
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Check
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%2
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12.
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Type
of Reporting Person (See Instructions)
HC,
IN
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1
The shares reported herein for the Reporting Person represent (i) 270,292 shares of the Issuer’s Common Stock beneficially
owned (ii) 1,057,000 shares of the Issuer’s Common Stock the Reporting Person has the right to acquire through the exercise
of pre-funded warrants (“Pre-Funded Warrants”) and (iii) 1,136,000 shares of the Issuer’s Common Stock the Reporting
Person has the right to acquire through the exercise of Class A Warrants (“Class A Warrants”). The Pre-Funded Warrants
and the Class A Warrants contain a provision (the “Beneficial Ownership Blocker”) which precludes exercise of the
warrants to the extent that, following exercise, the Reporting Person, together with its affiliates and other attribution parties,
would own more than 9.99% of the Common Stock Outstanding. As a result, the Reporting Person is currently prohibited from exercising
the warrants to the extent that exercise would result in ownership of more than 1,648,485 shares of Common Stock.
2 The number
of shares outstanding for purposes of this percentage calculation assumes (i) 16,102,872 outstanding shares of Common Stock of
the Issuer, based on the Issuer’s Form 424B5 Prospectus as filed with the Securities and Exchange Commission (“SEC”)
on November 27, 2019, plus (ii) 398,485 shares of Common Stock of which the Reporting Person may acquire beneficial ownership
upon the exercise of Pre-Funded Warrants and Class A Warrants, as limited by the Beneficial Ownership Blocker.
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1.
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Names
of Reporting Persons.
I.R.S. Identification Nos. of above persons (entities only).
Rajeev
Shah
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2.
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Check
the Appropriate Box if a Member of a Group (See Instructions)
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(a)
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¨
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(b)
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¨
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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
shares
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6.
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Shared
Voting Power 1,648,4851
shares
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7.
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Sole
Dispositive Power 0
shares
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8.
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Shared
Dispositive Power 1,648,4851 shares
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9.
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Aggregate
Amount Beneficially Owned by Each Reporting Person
1,648,4851
shares
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10.
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Check
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%2
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12.
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Type
of Reporting Person (See Instructions)
HC,
IN
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1The
shares reported herein for the Reporting Person represent (i) 270,292 shares of the Issuer’s Common Stock beneficially owned
(ii) 1,057,000 shares of the Issuer’s Common Stock the Reporting Person has the right to acquire through the exercise of
pre-funded warrants (“Pre-Funded Warrants”) and (iii) 1,136,000 shares of the Issuer’s Common Stock the Reporting
Person has the right to acquire through the exercise of Class A Warrants (“Class A Warrants”). The Pre-Funded Warrants
and the Class A Warrants contain a provision (the “Beneficial Ownership Blocker”) which precludes exercise of the
warrants to the extent that, following exercise, the Reporting Person, together with its affiliates and other attribution parties,
would own more than 9.99% of the Common Stock Outstanding. As a result, the Reporting Person is currently prohibited from exercising
the warrants to the extent that exercise would result in ownership of more than 1,648,485 shares of Common Stock.
2 The number
of shares outstanding for purposes of this percentage calculation assumes (i) 16,102,872 outstanding shares of Common Stock of
the Issuer, based on the Issuer’s Form 424B5 Prospectus as filed with the Securities and Exchange Commission (“SEC”)
on November 27, 2019, plus (ii) 398,485 shares of Common Stock of which the Reporting Person may acquire beneficial ownership
upon the exercise of Pre-Funded Warrants and Class A Warrants, as limited by the Beneficial Ownership Blocker.
Item 1.
(a) Name
of Issuer: X4 Pharmaceuticals, Inc. (the “Issuer”).
(b) Address
of the Issuer’s Principal Executive Offices: 955 Massachusetts Avenue, 4th Floor, Cambridge, MA 02139.
Item 2.
(a) Name of Person
Filing: This joint statement on Schedule 13G is being filed by RA Capital Management, L.P. (“RA Capital”), Peter
Kolchinsky, and Rajeev Shah. RA Capital, Dr. Kolchinsky, and Mr. Shah are collectively referred to herein as the “Reporting
Persons.”
The Common Stock reported herein includes Common Stock beneficially
owned directly by RA Capital Healthcare Fund, L.P. (the “Fund”) and Common Stock beneficially owned directly by a separately
managed account (the “Account”). RA Capital Healthcare Fund GP, LLC is the general partner of the Fund. The general
partner of RA Capital is RA Capital Management GP, LLC, of which Dr. Kolchinsky and Mr. Shah are the controlling persons. RA Capital
serves as investment adviser for the Fund and the Account and may be deemed a beneficial owner, for purposes of Section 13(d) of
the Securities Exchange Act of 1934 (the “Act”), of any securities of the Issuer held by the Fund and the Account.
The Fund has delegated to RA Capital the sole power to vote and the sole power to dispose of all securities held in the Fund’s
portfolio, including the shares of the Issuer’s Common Stock reported herein. Because the Fund has divested voting
and investment power over the reported securities it holds and may not revoke that delegation on less than 61 days’ notice,
the Fund disclaims beneficial ownership of the securities it holds for purposes of Section 13(d) of the Act and therefore
disclaim any obligation to report ownership of the reported securities under Section 13(d) of the Act. As managers of RA Capital,
Dr. Kolchinsky and Mr. Shah may be deemed beneficial owners, for purposes of Section 13(d) of the Act, of any securities of the
Issuer beneficially owned by RA Capital. RA Capital, Dr. Kolchinsky, and Mr. Shah disclaim beneficial ownership of the securities
reported in this Schedule 13G Statement (the “Statement”) other than for the purpose of determining their obligations
under Section 13(d) of the Act, and the filing of the Statement shall not be deemed an admission that either RA Capital, Dr. Kolchinsky,
or Mr. Shah is the beneficial owner of such securities for any other purpose.
(b) Address
of Principal Business Office: The principal business office of the Reporting Persons is c/o RA Capital Management, L.P., 200
Berkeley Street, 18th Floor, Boston, MA 02116.
(c) Citizenship:
RA Capital is a Delaware limited partnership. Dr. Kolchinsky and Mr. Shah are United States citizens.
(d) Title
and Class of Securities: Common stock (“Common Stock”)
(e) CUSIP
Number: 98420X103
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Item 3.
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If this statement is filed pursuant to §§240.13d-1(b) or 240.13d-2(b) or (c), check whether the person filing is a:
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(e) RA Capital Management, L.P. is a registered investment adviser
and is filing this statement in accordance with §240.13d-1(b)(1)(ii)(E);
(g) Peter Kolchinsky and Rajeev Shah are control persons and
are filing this statement in accordance with §240.13d-1(b)(1)(ii)(G).
Provide the following information regarding
the aggregate number and percentage of the class of securities of the issuer identified in Item 1.
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(a)
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Amount Beneficially Owned:
The Fund holds (i) 229,918 shares of Common Stock, (ii) Pre-Funded
Warrants with the right to acquire 898,873 shares of Common Stock and (iii) Class A Warrants with the right to acquire 966,054
shares of Common Stock. The Account holds (i) 40,374 shares of Common Stock, (ii) Pre-Funded Warrants with the right to acquire
158,127 shares of Common Stock and (iii) Class A Warrants with the right to acquire 169,946 shares of Common Stock. The Pre-Funded
Warrants and the Class A Warrants may not be exercised, however, to the extent that, following such exercise, the holders, together
with their affiliates and other attribution parties, including the Reporting Persons, would beneficially own more than 9.99% of
the Common Stock outstanding immediately following such exercise. Accordingly, the Pre-Funded Warrants and Class A Warrants held
by the Fund and the Account currently may not be exercised if, as a result of such exercise, the Reporting Persons would beneficially
own more than 1,648,485 shares of Common Stock.
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(b)
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Percent of Class:
See the response(s) to Item 11 on the attached cover page(s).
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(c)
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Number of shares as to which such person has:
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(i)
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sole power to vote or to direct the vote:
See the response(s) to Item 5 on the attached cover page(s).
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(ii)
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shared power to vote or to direct the vote
See the response(s) to Item 6 on the attached cover page(s).
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(iii)
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sole power to dispose or to direct the disposition of
See the response(s) to Item 7 on the attached cover page(s).
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(iv)
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shared power to dispose or to direct the disposition of
See the response(s) to Item 8 on the attached cover page(s).
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Item 5.
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Ownership of Five Percent or Less of a Class:
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Not applicable.
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Item 6.
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Ownership of More than Five Percent on Behalf of Another Person:
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Not applicable.
Item 7.
Identification and Classification of the Subsidiary Which Acquired the Security Being Reported on By the Parent Holding Company
or Control Person:
Not applicable.
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Item 8.
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Identification and Classification of Members of the Group:
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Not applicable.
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Item 9.
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Notice of Dissolution of Group:
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Not applicable.
By signing below I hereby 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.
SIGNATURE
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.
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Date: February
14, 2020
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RA CAPITAL MANAGEMENT, L.P.
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By:
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/s/ Peter Kolchinsky
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Peter Kolchinsky
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Authorized Signatory
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PETER KOLCHINSKY
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/s/ Peter Kolchinsky
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RAJEEV SHAH
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/s/ Rajeev Shah
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Exhibit 1
JOINT FILING AGREEMENT
This Joint Filing Agreement,
dated as of February 14, 2020, is by and among RA Capital Management, LLC and Peter Kolchinsky (the foregoing are collectively
referred to herein as the “Filers”).
Each of the Filers
may be required to file with the United States Securities and Exchange Commission a statement on Schedule 13G and/or 13D with respect
to Common Stock, par value $0.001 per share of X4 Pharmaceuticals, Inc. beneficially owned by them from time to time.
Pursuant to and in
accordance with Rule 13(d)(1)(k) promulgated under the Securities Exchange Act of 1934, as amended, the Filers hereby agree to
file a single statement on Schedule 13G and/or 13D (and any amendments thereto) on behalf of each of such parties, and hereby further
agree to file this Joint Filing Agreement as an exhibit to such statement, as required by such rule.
This Joint Filing Agreement
may be terminated by any of the Filers upon one week’s prior written notice or such lesser period of notice as the Filers
may mutually agree.
Executed and delivered
as of the date first above written.
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RA CAPITAL MANAGEMENT, L.P.
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By:
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/s/ Peter Kolchinsky
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Peter Kolchinsky
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Authorized Signatory
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PETER KOLCHINSKY
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/s/ Peter Kolchinsky
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RAJEEV SHAH
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/s/ Rajeev Shah
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