Sec Form 4 Filing - COLUMN GROUP II, LP @ RAPT Therapeutics, Inc. - 2024-12-23

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 Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934, Section 17(a) of the Public Utility Holding Company Act of 1935 or Section 30(h) of the Investment Company Act of 1940

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1. Name and Address of Reporting Person COLUMN GROUP II, LP 2. Issuer Name and Ticker or Trading Symbol RAPT Therapeutics, Inc. [ RAPT] 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 (Last) (First) (Middle) 1 LETTERMAN DRIVE, BUILDING D, SUITE DM-900 3. Date of Earliest Transaction (MM/DD/YY) 12/23/2024 (Street) SAN FRANCISCO, CA94129 4. If Amendment, Date Original Filed (MM/DD/YY) 6. Individual or Joint/Group Filing (Check Applicable Line) _____ Form filed by One Reporting Person __ X __ Form filed by More than One Reporting Person (City) (State) (Zip)

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned 1.Title of Security (Instr. 3) 2. Transaction Date (MM/DD/YY) 2A. Deemed Execution Date, if any (MM/DD/YY) 3. Transaction 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 12/23/2024 J( 1 ) 1,352,008 D 50,000 D ( 2 ) Common Stock 12/23/2024 J( 1 ) 1,599,417 D 0 I See footnote ( 3 ) Common Stock 1,236,261 I See footnote ( 4 ) Common Stock 42,189 I See footnote ( 5 ) Common Stock 163 I See footnote ( 6 ) Common Stock 145,401 I See footnote ( 7 )

Table II - Derivative Securities Acquired, Disposed of, or Beneficially Owned ( e.g. , puts, calls, warrants, options, convertible securities) 1. Title of Derivative Security (Instr. 3) 2. Conversion or Exercise Price of Derivative Security 3. Transaction Date (MM/DD/YY) 3A. Deemed Execution Date, if any (MM/DD/YY) 4. Transaction 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 (MM/DD/YY) 7. Title and Amount of Underlying Securities (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 Warrant (right to purchase) $ 0.0001 12/23/2024 J( 1 ) 1,352,008 ( 8 ) ( 8 ) Common Stock 1,352,008 ( 1 ) 1,352,008 D ( 2 ) Warrant (right to purchase) $ 0.0001 12/23/2024 J( 1 ) 1,599,417 ( 8 ) ( 8 ) Common Stock 1,599,417 ( 1 ) 1,599,417 I See footnote ( 3 )

Reporting Owners Reporting Owner Name / Address Relationships Director 10% Owner Officer Other COLUMN GROUP II, LP 1 LETTERMAN DRIVE BUILDING D, SUITE DM-900 SAN FRANCISCO, CA94129 Former 10% Owner Column Group II GP, LP 1 LETTERMAN DRIVE BUILDING D, SUITE DM-900 SAN FRANCISCO, CA94129 X PONOI CAPITAL, LP 1 LETTERMAN DRIVE BUILDING D, SUITE DM-900 SAN FRANCISCO, CA94129 X Ponoi Management, LLC 1 LETTERMAN DRIVE BUILDING D, SUITE DM-900 SAN FRANCISCO, CA94129 X Ponoi Capital II, LP 1 LETTERMAN DRIVE BUILDING D, SUITE DM-900 SAN FRANCISCO, CA94129 X Ponoi II Management, LLC 1 LETTERMAN DRIVE BUILDING D, SUITE DM-900 SAN FRANCISCO, CA94129 X Kutzkey Tim 1 LETTERMAN DRIVE BUILDING D, SUITE DM-900 SAN FRANCISCO, CA94129 X GOEDDEL DAVID V 1 LETTERMAN DRIVE BUILDING D, SUITE DM-900 SAN FRANCISCO, CA94129 X Svennilson Peter 1 LETTERMAN DRIVE BUILDING D, SUITE DM-900 SAN FRANCISCO, CA94129 X Column Group LLC 1 LETTERMAN DRIVE BUILDING D, SUITE DM-900 SAN FRANCISCO, CA94129 X Signatures /s/ James Evangelista, as Attorney-in-fact for David Goeddel 12/23/2024 Signature of Reporting Person Date /s/ James Evangelista, as Attorney-in-fact for Peter Svennilson 12/23/2024 Signature of Reporting Person Date /s/ James Evangelista, as Attorney-in-fact for Tim Kutzkey 12/23/2024 Signature of Reporting Person Date /s/ James Evangelista, as Attorney-in-fact for Ponoi Capital II LP 12/23/2024 Signature of Reporting Person Date /s/ James Evangelista, as Attorney-in-fact for Ponoi II Management LLC 12/23/2024 Signature of Reporting Person Date /s/ James Evangelista, as Attorney-in-fact for Ponoi Capital LP 12/23/2024 Signature of Reporting Person Date /s/ James Evangelista, as Attorney-in-fact for Ponoi Management LLC 12/23/2024 Signature of Reporting Person Date /s/ James Evangelista, as Attorney-in-fact for The Column Group II LP 12/23/2024 Signature of Reporting Person Date /s/ James Evangelista, as Attorney-in-fact for The Column Group II GP LP 12/23/2024 Signature of Reporting Person Date /s/ James Evangelista, as Attorney-in-fact for The Column Group LLC 12/23/2024 Signature of Reporting Person Date

Explanation of Responses:

( 1 )On December 23, 2024, The Column Group II, LP ("TCG II LP") and Ponoi Capital, LP ("Ponoi LP") entered into an exchange agreement with the Issuer pursuant to which TCG II LP and Ponoi LP exchanged, for no additional consideration, 1,352,008 and 1,599,417 shares of the Issuer's Common Stock, respectively, for a pre-funded warrant to purchase 1,352,008 and 1,599,417 shares of Common Stock, respectively (the "Pre-Funded Warrants"). The Pre-Funded Warrants were issued on December 23, 2024 and have an exercise price of $0.0001 per share. ( 2 )The securities are directly held by TCG II LP. The Column Group II GP, LP ("TCG II GP") is the general partner of TCG II LP and may be deemed to have voting, investment and dispositive power with respect to these securities. The managing partners of TCG II GP are David Goeddel and Peter Svennilson (collectively, the "TCG II GP Managing Partners"). The TCG II GP Managing Partners may be deemed to share voting and investment power with respect to such shares. TCG II GP and each of the TCG II GP Managing Partners disclaim beneficial ownership of these shares, except to the extent of their respective pecuniary interest in such shares. ( 3 )The securities are directly held by Ponoi LP. Ponoi Management, LLC ("Ponoi LLC") is the general partner of Ponoi LP and may be deemed to have voting, investment and dispositive power with respect to these securities. The managing partners of Ponoi LLC are David Goeddel, Peter Svennilson and Tim Kutzkey (collectively, the "Ponoi Managing Partners"). The Ponoi Managing Partners may be deemed to share voting and investment power with respect to such shares. Ponoi LLC and the each of the Ponoi Managing Partners disclaims beneficial ownership of these shares, except to the extent of their respective pecuniary interest in such shares. ( 4 )The securities are directly held by The Column Group IV, LP ("TCG IV LP"). The Column Group IV GP, LP ("TCG IV GP LP") is the general partner of TCG IV LP and may be deemed to have voting and investment power with respect to these securities. TCG IV GP LLC ("TCG IV LLC") is the general partner of TCG IV GP LP and the ultimate general partner of TCG IV LP and may be deemed to have voting and investment power with respect to these securities. The managing members of TCG IV LLC are David Goeddel, Peter Svennilson and Tim Kutzkey (collectively, the "TCG IV Managing Members"). The TCG IV Managing Members may be deemed to share voting and investment power with respect to such securities. TCG IV GP LP, TCG IV LLC and each of the TCG IV Managing Members disclaim beneficial ownership of these securities, except to the extent of their respective pecuniary interest in such securities. ( 5 )The securities are directly held by The Column Group IV-A, LP ("TCG IV-A LP"). TCG IV GP LP is the general partner of TCG IV-A LP and may be deemed to have voting and investment power with respect to these securities. TCG IV LLC is the general partner of TCG IV GP LP and the ultimate general partner of TCG IV-A LP and may be deemed to have voting and investment power with respect to these securities. The managing members of TCG IV LLC are the TCG IV Managing Members. The TCG IV Managing Members may be deemed to share voting and investment power with respect to such securities. TCG IV GP LP, TCG IV LLC and each of the TCG IV Managing Members disclaim beneficial ownership of these securities, except to the extent of their respective pecuniary interest in such securities. ( 6 )The securities are directly held The Column Group LLC ("TCG LLC"). The managing members of TCG LLC are the Ponoi Managing Partners. The Ponoi Managing Partners may be deemed to share voting and investment power with respect to such shares. Each of the Ponoi Managing Partners disclaims beneficial ownership of these shares, except to the extent of their respective pecuniary interest in such shares. ( 7 )The securities are directly held by Ponoi Capital II, LP ("Ponoi II LP"). Ponoi II Management, LLC ("Ponoi II LLC") is the general partner of Ponoi II LP and may be deemed to have voting, investment and dispositive power with respect to these securities. The managing partners of Ponoi II LLC are the Ponoi Managing Partners. The Ponoi Managing Partners may be deemed to share voting and investment power with respect to such shares. Ponoi II LLC and the each of the Ponoi Managing Partners disclaims beneficial ownership of these shares, except to the extent of their respective pecuniary interest in such shares. ( 8 )The Pre-Funded Warrant has no expiration date and is exercisable at any time after the date of issuance. Notwithstanding the foregoing, a holder of the Pre-Funded Warrant may not exercise the Pre-Funded Warrant if the holder, together with other persons whose beneficial ownership is aggregated for purposes of Section 13 or Section 16 under the Securities Exchange Act of 1934, as amended, would beneficially own more than 4.99% of the number of shares of Common Stock outstanding immediately after giving effect to such exercise.

Remarks: Due to SEC restrictions on the number of reporting owners, this is Form 1 of 2.

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).

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