Amendment: SEC Form SC 13G/A filed by Day One Biopharmaceuticals Inc.

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13G/A

Under the Securities Exchange Act of 1934

(Amendment No. 3)*

DAY ONE BIOPHARMACEUTICALS, INC.

(Name of Issuer)

COMMON STOCK, $0.0001 PAR VALUE

(Title of Class of Securities)

23954D 109

(CUSIP Number)

September 30, 2024

(Date of Event Which Requires Filing of This Statement)

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).

⁽¹⁾ As described in Item 4 below, Atlas Venture Fund XI, L.P., a Delaware limited partnership (“Atlas XI”) directly holds 4,806,826 shares of the Issuer’s Common Stock. Atlas Venture Associates XI, L.P., a Delaware limited partnership (“AVA XI LP”) and Atlas Venture Associates XI, LLC, a Delaware limited liability company (“AVA XI LLC” and together with Atlas XI and AVA XI LP, the “Fund XI Reporting Persons”) beneficially own the shares of the Issuer’s Common Stock held by Atlas XI. AVA XI LP is the general partner of Atlas XI and AVA XI LLC is the general partner of AVA XI LP. Each of AVA XI LP and AVA XI LLC has voting and dispositive power over the shares held by Atlas XI.

⁽²⁾ This percentage is calculated based upon 87,760,456 outstanding shares of Common Stock of the Issuer as of July 31, 2024, as reported in the Issuer’s Form 10-Q, filed with the Securities and Exchange Commission on August 2, 2024.

⁽¹⁾ As described in Item 4 below, Atlas XI and AVA XI LP hold 4,806,826 and 62,855 shares of the Issuer’s Common Stock, respectively. AVA XI LP is the general partner of Atlas XI and AVA XI LLC is the general partner of AVA XI LP. Each of AVA XI LP and AVA XI LLC has voting and dispositive power over the shares held by Atlas XI and AVA XI LLC has voting and dispositive power over the shares held by AVA XI LP.

⁽²⁾ This percentage is calculated based upon 87,760,456 outstanding shares of Common Stock of the Issuer as of July 31, 2024, as reported in the Issuer’s Form 10-Q, filed with the Securities and Exchange Commission on August 2, 2024.

⁽¹⁾ As described in Item 4 below, Atlas XI and AVA XI LP hold 4,806,826 and 62,855 shares of the Issuer’s Common Stock, respectively. AVA XI LP is the general partner of Atlas XI and AVA XI LLC is the general partner of AVA XI LP. Each of AVA XI LP and AVA XI LLC has voting and dispositive power over the shares held by Atlas XI and AVA XI LLC has voting and dispositive power over the shares held by AVA XI LP.

⁽²⁾ This percentage is calculated based upon 87,760,456 outstanding shares of Common Stock of the Issuer as of July 31, 2024, as reported in the Issuer’s Form 10-Q, filed with the Securities and Exchange Commission on August 2, 2024.

⁽¹⁾ As described in Item 4 below, Atlas Venture Opportunity Fund I, L.P., a Delaware limited partnership (“AVO I”) directly holds 793,116 shares of the Issuer’s Common Stock. Atlas Venture Associates Opportunity I, L.P., a Delaware limited partnership (“AVAO LP”) is the general partner of AVO I and Atlas Venture Associates Opportunity I, LLC, a Delaware limited liability company (“AVAO LLC” and together with AVO I and AVAO LP, the “Opportunity Fund Reporting Persons”) beneficially own the shares of the Issuer’s Common Stock held by AVO I. AVAO LP is the general partner of AVO I and AVAO LLC is the general partner of AVAO LP. Each of AVAO LP and AVAO LLC has voting and dispositive power over the shares held by AVO I.

⁽²⁾ This percentage is calculated based upon 87,760,456 outstanding shares of Common Stock of the Issuer as of July 31, 2024, as reported in the Issuer’s Form 10-Q, filed with the Securities and Exchange Commission on August 2, 2024.

⁽¹⁾ As described in Item 4 below, AVO I and AVAO LP hold 793,116 and 793 shares of the Issuer’s Common Stock, respectively. AVAO LP is the general partner of AVO I and AVAO LLC is the general partner of AVAO LP. Each of AVAO LP and AVAO LLC has voting and dispositive power over the shares held by AVO I and AVAO LLC has voting and dispositive power over the shares held by AVAO LP.

⁽²⁾ This percentage is calculated based upon 87,760,456 outstanding shares of Common Stock of the Issuer as of July 31, 2024, as reported in the Issuer’s Form 10-Q, filed with the Securities and Exchange Commission on August 2, 2024.

⁽¹⁾ As described in Item 4 below, AVO I and AVAO LP hold 793,116 and 793 shares of the Issuer’s Common Stock, respectively. AVAO LP is the general partner of AVO I and AVAO LLC is the general partner of AVAO LP. Each of AVAO LP and AVAO LLC has voting and dispositive power over the shares held by AVO I and AVAO LLC has voting and dispositive power over the shares held by AVAO LP.

⁽²⁾ This percentage is calculated based upon 87,760,456 outstanding shares of Common Stock of the Issuer as of July 31, 2024, as reported in the Issuer’s Form 10-Q, filed with the Securities and Exchange Commission on August 2, 2024.

⁽¹⁾ As described in Item 4 below, Atlas Venture Opportunity Fund II, L.P., a Delaware limited partnership (“AVO II”) directly holds 766,667 shares of the Issuer’s Common Stock. Atlas Venture Associates Opportunity II, L.P., a Delaware limited partnership (“AVAO II LP”) and Atlas Venture Associates Opportunity II, LLC, a Delaware limited liability company (“AVAO II LLC” and together with AVO II and AVAO II LP, the “Opportunity Fund II Reporting Persons”) beneficially own the shares of the Issuer’s Common Stock held by AVO II. AVAO II LP is the general partner of AVO II and AVAO II LLC is the general partner of AVAO II LP. Each of AVAO II LP and AVAO II LLC has voting and dispositive power over the shares held by AVO II. As such, each of the Opportunity Fund II Reporting Persons share voting and dispositive power with respect to the shares held by AVO II.

⁽²⁾ This percentage is calculated based upon 87,760,456 outstanding shares of Common Stock of the Issuer as of July 31, 2024, as reported in the Issuer’s Form 10-Q, filed with the Securities and Exchange Commission on August 2, 2024.

⁽¹⁾ As described in Item 4 below, AVO II, AVAO II LP and AVAO II LLC beneficially own 766,667 shares of the Issuer’s Common Stock. All of these shares are directly held by AVO II. AVAO II LP is the general partner of AVO II and AVAO II LLC is the general partner of AVAO II LP. Each of AVAO II LP and AVAO II LLC has voting and dispositive power over the shares held by AVO II. As such, each of the Opportunity Fund II Reporting Persons share voting and dispositive power with respect to the shares held by AVO II.

⁽²⁾ This percentage is calculated based upon 87,760,456 outstanding shares of Common Stock of the Issuer as of July 31, 2024, as reported in the Issuer’s Form 10-Q, filed with the Securities and Exchange Commission on August 2, 2024.

⁽¹⁾ As described in Item 4 below, AVO II, AVAO II LP and AVAO II LLC beneficially own 766,667 shares of the Issuer’s Common Stock. All of these shares are directly held by AVO II. AVAO II LP is the general partner of AVO II and AVAO II LLC is the general partner of AVAO II LP. Each of AVAO II LP and AVAO II LLC has voting and dispositive power over the shares held by AVO II. As such, each of the Opportunity Fund II Reporting Persons share voting and dispositive power with respect to the shares held by AVO II.

⁽²⁾ This percentage is calculated based upon 87,760,456 outstanding shares of Common Stock of the Issuer as of July 31,2024, as reported in the Issuer’s Form 10-Q, filed with the Securities and Exchange Commission on August 2, 2024.

Day One Biopharmaceuticals, Inc. (the “Issuer”)

2000 Sierra Point Parkway Suite 501
Brisbane, CA, 94005

This Schedule 13G is filed by (i) Atlas Venture Fund XI, L.P., a Delaware limited partnership (“Atlas XI”), (ii) Atlas Venture Associates XI, L.P., a Delaware limited partnership (“AVA XI LP”), (iii) Atlas Venture Associates XI, LLC, a Delaware limited liability company (“AVA XI LLC” and together with Atlas XI and AVA XI LP, the “Fund XI Reporting Persons”), (iv) Atlas Venture Opportunity Fund I, L.P., a Delaware limited partnership (“AVO I”), (v) Atlas Venture Associates Opportunity I, L.P., a Delaware limited partnership (“AVAO LP”), (vi) Atlas Venture Associates Opportunity I, LLC, a Delaware limited liability company (“AVAO LLC” and together with AVO I and AVAO LP, the “Opportunity Fund Reporting Persons”), (vii) Atlas Venture Opportunity Fund II, L.P., a Delaware limited partnership (“AVO II”), (viii) Atlas Venture Associates Opportunity II, L.P., a Delaware limited partnership (“AVAO II LP”) and (ix) Atlas Venture Associates Opportunity II, LLC, a Delaware limited liability company (“AVAO II LLC” and together with AVO II and AVAO II LP, the “Opportunity Fund II Reporting Persons” and together with the Fund XI Reporting Persons and Opportunity Fund Reporting Persons, the "Reporting Persons”).

300 Technology Square, 8th Floor
Cambridge, Massachusetts 02139

Each of Atlas XI, AVA XI LP, AVO I, AVAO LP, AVO II and AVAO II LP is a Delaware limited partnership.
Each of AVA XI LLC, AVAO LLC and AVAO II LLC is a Delaware limited liability company.

Common Stock, $0.0001 par value per share

23954D 109

Item 3

Not applicable.

Provide the following information regarding the aggregate number and percentage of the class of securities of the issuer identified in Item 1

Amount beneficially owned: AVA XI LP is the record owner of 62,855 shares of Common Stock. AVA XI LLC is the general partner of AVA XI LP. Each of AVA XI LP and AVA XI LLC has shared voting and dispositive power over the shares held by AVA XI LP. As such, each of AVA XI LP and AVA XI LLC may be deemed to beneficially own the shares held by AVA XI LP.

Amount beneficially owned: AVO I is the record owner of 793,116 shares of Common Stock. AVAO LP is the general partner of AVO I and AVAO LLC is the general partner of AVAO LP. Each of AVO I, AVAO LP and AVAO LLC has shared voting and dispositive power over the shares held by AVO I. As such, each of AVO I, AVAO LP and AVAO LLC may be deemed to beneficially own the shares held by AVO I.

Amount beneficially owned: AVAO LP is the record owner of 793 shares of Common Stock. AVAO LLC is the general partner of AVAO LP. Each of AVAO LP and AVAO LLC has shared voting and dispositive power over the shares held by AVAO LP. As such, each of AVAO LP and AVAO LLC may be deemed to beneficially own the shares held by AVAO LP.

Amount beneficially owned: AVO II is the record owner of 766,667 shares of Common Stock. AVAO II LP is the general partner of AVO II and AVAO II LLC is the general partner of AVAO II LP. Each of AVO II, AVAO II LP and AVAO II LLC has shared voting and dispositive power over the shares held by AVO II. As such, each of AVO II, AVAO II LP and AVAO II LLC may be deemed to beneficially own the shares held by AVO II.

Each of the Opportunity Fund Reporting Persons may be deemed to beneficially own 0.9% of the Issuer’s outstanding Common Stock.

Each of the Opportunity Fund II Reporting Persons may be deemed to beneficially own 0.9% of the Issuer’s outstanding Common Stock.

These percentages are calculated based upon 87,760,456 outstanding shares of Common Stock of the Issuer as of July 31, 2024, as reported in the Issuer’s Form 10-Q, filed with the Securities and Exchange Commission on August 2, 2024.

Collectively, the Reporting Persons beneficially own an aggregate of 6,430,257 shares of Common Stock, which represents 7.3% of the Issuer's outstanding Common Stock. The Fund XI Reporting Persons, the Opportunity Fund Reporting Persons and the Opportunity Fund II Reporting Persons are under common control and as a result, the Reporting Persons may be deemed to be members of a group. However, the Reporting Persons disclaim such group membership, and this Schedule 13G shall not be deemed an admission that the Reporting Persons are members of a group for purposes of Section 13 or for any other purposes.

Each of AVA XI LP and AVA XI LLC shares power to vote or direct the vote of 4,869,681 shares of Common Stock.

AVO I shares power to vote or direct the vote of 793,116 shares of Common Stock.

Each of AVAO LP and AVAO LLC shares power to vote or direct the vote of 793,909 shares of Common Stock.

Each of the Opportunity Fund II Reporting Persons shares power to vote or direct the vote of 766,667 shares of Common Stock.

Each of AVA XI LP and AVA XI LLC shares power to dispose or to direct the disposition of 4,869,681 shares of Common Stock.

AVO I shares power to dispose or to direct the disposition of 793,116 shares of Common Stock.

Each of AVAO LP and AVAO LLC shares power to dispose or to direct the disposition of 793,909 shares of Common Stock.

Each of the Opportunity Fund II Reporting Persons shares power to dispose or to direct the disposition of 766,667 shares of Common Stock.

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. ¨

Not applicable.

Not applicable.

Not applicable.

 Not applicable.

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, other than activities solely in connection with a nomination under § 240.14a-11.

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.

Dated: November 14, 2024

EXHIBITS