[SCHEDULE 13D/A] Kymera Therapeutics, Inc. SEC Filing

Rhea-AI Filing Summary

Baker Bros. Advisors LP and affiliates have filed Amendment No. 2 to Schedule 13D disclosing a 9.5% beneficial stake in Kymera Therapeutics, Inc. (KYMR). The group – Baker Bros. Advisors LP, Baker Bros. Advisors (GP) LLC, and principals Julian C. Baker and Felix J. Baker – now control 6,666,540 shares of common stock, based on 70,157,214 shares outstanding as of 30 Jun 2025.

Recent transaction. On 26 Jun 2025 Kymera priced a public offering of 5,044,500 shares at $44.00 and 655,500 prefunded warrants at $43.9999. Funds managed by Baker Bros. purchased 655,500 common shares and 655,500 prefunded warrants (split 55,191/600,309 between 667 LP and Life Sciences LP). The offering closed 30 Jun 2025.

• Voting / dispositive power: Sole voting and dispositive power over all 6.67 M shares.
• Prefunded warrants: 1-for-1 conversion at $0.0001, exercisable indefinitely but capped at a 4.99% ownership limit (adjustable up to 19.99% with 61 days’ notice).
• Registration rights: Funds obtained shelf and underwritten offering rights (up to three offerings over ten years) effective from 28 Feb 2026.
• Director lock-up: Felix Baker agreed not to sell KYMR securities until 24 Sep 2025 (subject to customary exceptions).

The filing emphasises that the position is investment-motivated; the funds may buy or sell additional securities depending on prevailing conditions, and no plans for extraordinary corporate actions are currently disclosed.

Positive

• High-calibre biotech investor Baker Bros. increased ownership to 9.5%, signalling conviction in KYMR’s prospects.
• $57.3 m direct purchase in the June offering strengthens Kymera’s cash position and reduces capital risk.
• 90-day lock-up on Felix Baker’s holdings limits near-term selling pressure.

Negative

• Potential dilution: 655,500 prefunded warrants and stock options could add ~0.9% to share count once exercisable.
• Registration rights enable future secondary sales after Feb 2026, which may create overhang.

Insights

Biotechnology Portfolio Manager

TL;DR – Baker Bros. lifts KYMR stake to 9.5%, signals confidence via $44 follow-on purchase.

The Bakers are among the most respected specialist investors in biotech, often taking concentrated positions in late-platform stories. Their decision to absorb roughly 13% of the follow-on ($57.3 m of the $222 m equity raise) materially reduces financing overhang risk for Kymera and aligns the company with a supportive long-term holder. Registration rights and a 90-day lock-up suggest the investment horizon is at least mid-term. While the 4.99% warrant cap limits near-term dilution, the eventual exercise could add ~0.9% to the share count. Overall, this ownership update is incrementally positive for sentiment and improves Kymera’s balance-sheet flexibility.

Corporate Governance & Risk Analyst

TL;DR – Neutral governance impact; potential future dilution modest but monitor warrant cap.

The filing contains no activism trigger or board change. Control remains below the 10% threshold that could attract heightened scrutiny. Prefunded warrants are typical in life-science financing, though investors should watch the Beneficial Ownership Limitation: a future notice could allow the funds to lift ownership to 19.99%, increasing influence. The director lock-up mitigates immediate resale risk, but registration rights from Feb 2026 could accelerate secondary offerings. Impact on corporate control is therefore neutral at present, with modest dilution risk.

SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 2)

Kymera Therapeutics, Inc.

(Name of Issuer)

Common Stock, $0.0001 par value per share

(Title of Class of Securities)

501575104

(CUSIP Number)

Alexandra A. Toohey, CFO
860 Washington Street, 3rd Floor,
New York, NY, 10014
212-339-5690

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

06/26/2025

(Date of Event Which Requires Filing of This Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§ 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box.

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).

SCHEDULE 13D

CUSIP No. 501575104

1

Name of reporting person

Baker Bros. Advisors LP

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

OO

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

DELAWARE

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 6,666,540.00
8	Shared Voting Power 0.00
9	Sole Dispositive Power 6,666,540.00
10	Shared Dispositive Power 0.00

11

Aggregate amount beneficially owned by each reporting person

6,666,540.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

9.5 %

14

Type of Reporting Person (See Instructions)

IA, PN

SCHEDULE 13D

CUSIP No. 501575104

1

Name of reporting person

Baker Bros. Advisors (GP) LLC

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

OO

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

DELAWARE

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 6,666,540.00
8	Shared Voting Power 0.00
9	Sole Dispositive Power 6,666,540.00
10	Shared Dispositive Power 0.00

11

Aggregate amount beneficially owned by each reporting person

6,666,540.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

9.5 %

14

Type of Reporting Person (See Instructions)

HC, OO

SCHEDULE 13D

CUSIP No. 501575104

1

Name of reporting person

Julian C. Baker

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

OO

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

UNITED STATES

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 6,666,540.00
8	Shared Voting Power 0.00
9	Sole Dispositive Power 6,666,540.00
10	Shared Dispositive Power 0.00

11

Aggregate amount beneficially owned by each reporting person

6,666,540.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

9.5 %

14

Type of Reporting Person (See Instructions)

IN, HC

SCHEDULE 13D

CUSIP No. 501575104

1

Name of reporting person

Felix J. Baker

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

OO

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

UNITED STATES

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 6,666,540.00
8	Shared Voting Power 0.00
9	Sole Dispositive Power 6,666,540.00
10	Shared Dispositive Power 0.00

11

Aggregate amount beneficially owned by each reporting person

6,666,540.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

9.5 %

14

Type of Reporting Person (See Instructions)

IN, HC

SCHEDULE 13D

Item 1.	Security and Issuer
(a)	Title of Class of Securities: Common Stock, $0.0001 par value per share
(b)	Name of Issuer: Kymera Therapeutics, Inc.
(c)	Address of Issuer's Principal Executive Offices: 500 North Beacon Street, 4th Floor, Watertown, MASSACHUSETTS , 02472.
Item 1 Comment: This Amendment No. 2 to Schedule 13D amends and supplements the previously filed Schedule 13D filed by Baker Bros. Advisors LP (the "Adviser"), Baker Bros. Advisors (GP) LLC (the "Adviser GP"), Julian C. Baker and Felix J. Baker (collectively, the "Reporting Persons"). Except as supplemented herein, such statements, as heretofore amended and supplemented, remain in full force and effect. The Adviser GP is the sole general partner of the Adviser. Pursuant to management agreements, as amended, among the Adviser, Baker Brothers Life Sciences, L.P. ("Life Sciences") and 667, L.P. ("667", and together with Life Sciences, the "Funds"), and their respective general partners, the Funds' respective general partners relinquished to the Adviser all discretion and authority with respect to the investment and voting power of the securities held by the Funds, and thus the Adviser has complete and unlimited discretion and authority with respect to the Funds' investments and voting power over investments. All capitalized terms contained herein but not otherwise defined shall have the meanings ascribed to such terms in the Schedule 13D, as amended. Information given in response to each item shall be deemed incorporated by reference in all other items, as applicable.
Item 3.	Source and Amount of Funds or Other Consideration
	Item 3 of Schedule 13D is supplemented and amended, as the case may be, as follows: The Reporting Persons may in the ordinary course of business hold securities in margin accounts maintained for the Funds with prime brokers, which extend margin credit as and when required, subject to applicable margin regulations, stock exchange rules and such firms' credit policies. Positions in securities may be pledged as collateral security for the repayment of debit balances in such accounts.
Item 4.	Purpose of Transaction
	Item 4 of Schedule 13D is supplemented and amended, as the case may be, as follows: The disclosure in Item 3 and in Item 6 below is incorporated herein by reference. On June 26, 2025, the Issuer entered into an underwriting agreement (the "Underwriting Agreement") with Morgan Stanley & Co. LLC, J.P. Morgan Securities LLC, Jefferies LLC, TD Securities (USA) LLC and Leerink Partners LLC (the "Underwriters"), related to the public offering (the "Offering") of 5,044,500 shares of common stock of the Issuer ("Common Stock") at a price to the public of $44.00 per share and prefunded warrants to purchase 655,500 shares of Common Stock (the "Prefunded Warrants") at a price to the public of $43.9999 per warrant. The Prefunded Warrants are exercisable at any time on a 1-for-1 basis at an exercise price of $0.0001 per share into Common Stock, subject to the limitations discussed below and have no expiration date. In addition, the Issuer granted the Underwriters an option exercisable for 30 days from the date of the Underwriting Agreement to purchase, at the public offering price less any underwriting discounts and commissions, up to an additional 855,000 shares of Common Stock to cover overallotments, if any ("Underwriters Option"). The Offering closed on June 30, 2025. Pursuant to the Offering, 667 and Life Sciences purchased 55,191 and 600,309 shares of Common Stock, respectively, at the offering price of $44.00 per share, totaling 655,500 shares of Common Stock in the aggregate and 55,191 and 600,309 Prefunded Warrants, respectively, at the offering price of $43.9999 per warrant, totaling 655,500 Prefunded Warrants in the aggregate. Each of 667 and Life Sciences purchased the Common Stock and Prefunded Warrants with their working capital. The Funds hold securities of the Issuer for investment purposes. The Reporting Persons or their affiliates may purchase additional securities or dispose of securities in varying amounts and at varying times depending upon the Reporting Persons' continuing assessments of pertinent factors, including the availability of shares of Common Stock or other securities for purchase at particular price levels, the business prospects of the Issuer, other business investment opportunities, economic conditions, stock market conditions, money market conditions, the attitudes and actions of the board of directors of the Issuer (the "Board") and management of the Issuer, the availability and nature of opportunities to dispose of securities of the Issuer and other plans and requirements of the particular entities. The Reporting Persons may discuss items of mutual interest with the Issuer's management, other members of the Board and other investors, which could include items in subparagraphs (a) through (j) of Item 4 Schedule 13D. Depending upon their assessments of the above factors, the Reporting Persons or their affiliates may change their present intentions as stated above and they may assess whether to make suggestions to the management of the Issuer regarding financing, and whether to acquire additional securities of the Issuer, including shares of Common Stock (by means of open market purchases, privately negotiated purchases, exercise of Prefunded Warrants (as defined in Item 4), or otherwise), exercise of some or all of the Stock Options (as defined below) to purchase Common Stock of the Issuer or to dispose of some or all of the securities of the Issuer, including shares of Common Stock, under their control. Except as otherwise disclosed herein, at the present time, the Reporting Persons do not have any plans or proposals with respect to any extraordinary corporate transaction involving the Issuer including, without limitation, those matters described in subparagraphs (a) through (j) of Item 4 of Schedule 13D.
Item 5.	Interest in Securities of the Issuer
(a)	The disclosure in Item 4 is incorporated by reference herein. Item 5 of Schedule 13D is supplemented and amended, as the case may be, as follows: (a) and (b) Items 7 through 11 and 13 of each of the cover pages of this Amendment No. 2 are incorporated herein by reference. The percentage of beneficial ownership for each of the Reporting Persons reported herein is based on 70,157,214 shares of Common Stock outstanding as of June 30, 2025 as reported in the Issuer's Prospectus filed with the Securities and Exchange Commission ("SEC") on June 27, 2025 plus 15,111 vested non-qualified options exercisable for 15,111 shares of Common Stock ("Stock Options") received by Felix J. Baker as compensation for his service on the Board. Set forth below in Exhibit 99.1 is the aggregate number of shares of Common Stock directly held by each of the Funds, which may be deemed to be indirectly beneficially owned by the Reporting Persons, as well as shares of Common Stock that may be acquired upon exercise of Prefunded Warrants, subject to the Beneficial Ownership Limitation (as defined below).
(b)	The direct holdings of the Funds are detailed in Exhibit 99.1. The Prefunded Warrants are only exercisable to the extent that after giving effect to such exercise the holders thereof, together with their affiliates and any members of a Section 13(d) group with such holders, would beneficially own, for purposes of Rule 13d-3 under the Securities Exchange Act of 1934, as amended (the "Exchange Act"), no more than 4.99% of the outstanding shares of Common Stock (the "Beneficial Ownership Limitation"). By written notice to the Issuer, the Funds may from time to time increase or decrease the Beneficial Ownership Limitation applicable to that Fund to any other percentage not in excess of 19.99%. Any such increase will not be effective until the 61st day after such notice is delivered to the Issuer. As a result of this restriction, the number of shares that may be issued upon exercise of the Prefunded Warrants by the above holders may change depending upon changes in the number of outstanding shares of Common Stock. The Prefunded Warrants are not currently exercisable due to the effect of the Beneficial Ownership Limitation. The foregoing description of the Prefunded Warrants is qualified in its entirety by reference to the full texts of the Form of Pre-Funded Warrant to Purchase Common Stock, which is incorporated by reference as Exhibit 99.2, and which is incorporated herein by reference. In conjunction with his service on the Board, Felix J. Baker holds 32,000 Stock Options at an exercise price of $40.20 per share which vest in 36 equal monthly installments over a three-year period commencing on March 28, 2024 and expire on March 27, 2034, of which 15,111 are vested as of sixty days following the date of this filing. On June 25, 2025, Felix J. Baker was granted 16,000 Stock Options at an exercise price of $46.47 that vest on the earlier of the first anniversary of the grant date or the date of the 2026 annual meeting of stockholders of the Issuer. Felix J. Baker also serves on the Compensation Committee of the Board. The policies of the Funds and the Adviser do not permit managing members of the Adviser GP to receive compensation for serving as a director of the Issuer, and the Funds are instead entitled to the pecuniary interest in any compensation received for Felix J. Baker's service on the Board. The Adviser GP, and Felix J. Baker and Julian C. Baker as managing members of the Adviser GP, may be deemed to have the power to vote or direct the vote of and the power to dispose or direct the disposition of the Stock Options held by Felix J. Baker disclosed herein and in previous amendments to this Schedule 13D. The Adviser GP, Felix J. Baker and Julian C. Baker as managing members of the Adviser GP, and the Adviser may be deemed to be beneficial owners of securities of the Issuer directly held by the Funds.
(c)	(c) Except as disclosed herein the Reporting Persons or their affiliates have not effected any transactions in securities of the Issuer during the past 60 days.
(d)	(d) Certain securities of the Issuer are held directly by 667, a limited partnership the sole general partner of which is Baker Biotech Capital, L.P., a limited partnership the sole general partner of which is Baker Biotech Capital (GP), LLC. Julian C. Baker and Felix J. Baker are the managing members of Baker Biotech Capital (GP), LLC. Certain securities of the Issuer are held directly by Life Sciences, a limited partnership the sole general partner of which is Baker Brothers Life Sciences Capital, L.P., a limited partnership the sole general partner of which is Baker Brothers Life Sciences Capital (GP), LLC. Julian C. Baker and Felix J. Baker are the managing members of Baker Brothers Life Sciences Capital (GP), LLC.
(e)	(e) Not applicable.
Item 6.	Contracts, Arrangements, Understandings or Relationships With Respect to Securities of the Issuer
	Item 6 of Schedule 13D is supplemented and amended, as the case may be, as follows: Prefunded Warrants The disclosure in Item 5 regarding the Prefunded Warrants is incorporated herein by reference. The foregoing description of the Prefunded Warrants is qualified in its entirety by reference to the full text of the form of Pre-Funded Warrant to Purchase Common Stock, which is incorporated by reference as Exhibit 99.2 hereto and is incorporated herein by reference. Registration Rights Agreement On June 26, 2025, the Funds and certain other investors entered into a registration rights agreement (the "Registration Rights Agreement") with the Issuer pursuant to which the Funds are entitled to certain resale registration rights with respect to all securities of the Company (whether equity, debt, or otherwise) and any Common Stock issued or issuable upon the exercise or conversion of any such securities that is now owned or hereafter acquired by the Funds or such other investors (collectively, the "Registrable Securities"). Under the Registration Rights Agreement, as promptly as reasonably practicable following a request by the Funds, the Issuer is obligated to file a resale registration statement on Form S-3, or other appropriate form, covering Registrable Securities held by the Funds (the "Resale Registration Shelf") (provided the Company shall not be obligated to make any such filing until February 28, 2026 (the "Demand Effective Date")), and to use reasonable best efforts to keep the Resale Registration Shelf effective until the earlier of such time that (i) all Registrable Securities covered by the Resale Registration Shelf have been sold or may be sold freely without limitations or restrictions as to volume or manner of sale pursuant to Rule 144 of the Securities Act of 1933, as amended, or (ii) all Registrable Securities covered by the Resale Registration Shelf otherwise cease to be considered Registrable Securities pursuant to the terms of the Registration Rights Agreement. Under the Registration Rights Agreement, the Funds have the right to (i) one underwritten public offering per calendar year, but no more than three underwritten public offerings in total, and (ii) no more than two underwritten public offerings or block trades in any twelve-month period, to effect the sale or distribution of Registrable Securities, subject to specified exceptions, conditions and limitations. The rights of the Funds under the Registration Rights Agreement will continue in effect for up to ten years following the Demand Effective Date. The foregoing description of the Registration Rights Agreement does not purport to be complete and is qualified in its entirety by reference to the full text of the Registration Rights Agreement, which is incorporated by reference as Exhibit 99.3 and is incorporated herein by reference. Director Lock-Up Agreement On June 26, 2025, Felix Baker entered into a Lock-Up Agreement (the "Director Lock-Up Agreement") pursuant to which, subject to specified exceptions, Dr. Baker in his personal capacity agreed, without the prior written consent of the representatives of the Underwriters, not to (1) offer, pledge, sell, contract to sell, sell any option or contract to purchase, purchase any option or contract to sell, grant any option, right or warrant to purchase, lend, or otherwise transfer or dispose of, directly or indirectly, any of his Common Stock or any of his other securities convertible into or exercisable or exchangeable for Common Stock or (2) enter into any swap or other arrangement that transfers to another, in whole or in part, any of the economic consequences of ownership of such Common Stock, in each case for a period beginning on June 26, 2025 and continuing until September 24, 2025. The foregoing description of the Director Lock-Up Agreement is qualified in its entirety by reference to the full text of the form of Director Lock-Up Agreement, which is incorporated by reference as Exhibit 99.4 and is incorporated herein by reference
Item 7.	Material to be Filed as Exhibits.
	99.1 Holdings by the Funds in Securities of the Issuer 99.2 Form of Pre-Funded Warrant to Purchase Common Stock (incorporated by reference to Exhibit 4.1 to the Issuer's Current Report on Form 8-K, filed with the SEC on June 27, 2025). 99.3 Registration Rights Agreement, by and among Kymera Therapeutics, Inc., 667, L.P., Baker Brothers Life Sciences, L.P., and certain other investors, dated as of June 26, 2025 (incorporated by reference to Exhibit 10.1 to the Issuer's Current Report on Form 8-K, filed with the SEC on June 27, 2025). 99.4 Form of Lock-Up Agreement (incorporated by reference to Exhibit A to Exhibit 1.1 to the Issuer's Current Report on Form 8-K, filed with the SEC on June 27, 2025).

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.

Baker Bros. Advisors LP

Signature:	/s/ Scott L. Lessing
Name/Title:	Scott L. Lessing/ President By: Baker Bros. Advisors (GP) LLC, its general partner
Date:	06/30/2025

Baker Bros. Advisors (GP) LLC

Signature:	/s/ Scott L. Lessing
Name/Title:	Scott L. Lessing/ President
Date:	06/30/2025

Julian C. Baker

Signature:	/s/ Julian C. Baker
Name/Title:	Julian C. Baker
Date:	06/30/2025

Felix J. Baker

Signature:	/s/ Felix J. Baker
Name/Title:	Felix J. Baker
Date:	06/30/2025

FAQ

How much of Kymera Therapeutics (KYMR) does Baker Bros. now own?

According to Amendment No. 2, the group beneficially owns 6,666,540 shares, or 9.5% of KYMR’s outstanding stock.

What price did Baker Bros. pay in the June 2025 Kymera offering?

They bought common shares at $44.00 each and prefunded warrants at $43.9999 per warrant.

When can Baker Bros. exercise its prefunded warrants in KYMR?

The warrants are exercisable at any time but capped at 4.99% ownership; the cap can be raised (max 19.99%) with 61 days’ notice.

Are Baker Bros. restricted from selling KYMR shares?

Felix Baker agreed to a lock-up until 24 Sep 2025; other shares can be traded at the funds’ discretion subject to market conditions.

What registration rights did Baker Bros. secure?

Starting 28 Feb 2026, the funds may demand shelf registration and up to three underwritten offerings over ten years for their KYMR holdings.