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

Rhea-AI Filing Summary

RA Capital Management, its principals Peter Kolchinsky and Rajeev Shah, and RA Capital Healthcare Fund report beneficial ownership of 3,365,523 shares of Cidara Therapeutics common stock, representing 13.3% of 25,358,051 shares outstanding. The Fund also holds Series A preferred stock convertible into up to 6,296,920 common shares and pre-funded warrants exercisable for up to 1,286,786 common shares, but conversion and exercise are limited by contractual Beneficial Ownership Blockers that prevent the Fund from owning more than 9.99% of the common stock and currently prohibit conversion or exercise.

RA Capital is the investment adviser with sole power to vote and dispose of the Fund’s reported securities, and the Fund has delegated those powers and disclaims beneficial ownership for Section 13(d) purposes. No transactions have been reported since the prior amendment; the reported percentage reflects an increase in the issuer’s outstanding shares.

Positive

• Material reported stake: 3,365,523 shares representing 13.3% of common stock
• Additional convertible exposure: Preferred convertible into up to 6,296,920 shares and pre-funded warrants exercisable for up to 1,286,786 shares
• Adviser control: RA Capital has sole power to vote and dispose of the Fund’s reported securities

Negative

• Conversion limited: Beneficial Ownership Blockers currently prevent conversion of Preferred Stock and exercise of Pre-Funded Warrants to avoid exceeding 9.99%
• Disclaimer of beneficial ownership: The Fund disclaims beneficial ownership for Section 13(d) purposes due to delegation, which may complicate clarity of reported ownership status

Insights

Financial Analyst

TL;DR: RA Capital reports a material 13.3% stake plus convertible instruments, though conversion is blocked by ownership limits.

The filing shows a material equity position of 3,365,523 shares (13.3%) and additional convertible exposure of up to 7,583,706 potential shares (preferred plus pre-funded warrants) subject to contractual ownership limits. The Beneficial Ownership Blockers prevent conversion/exercise above 9.99%, meaning the Fund cannot currently increase its common share stake via those instruments. RA Capital’s delegation of voting and dispositive power over the Fund’s holdings centralizes control with the adviser, while the Fund disclaims beneficial ownership for Section 13(d) reporting purposes. No new transactions were reported in this amendment.

Corporate Governance Expert

TL;DR: A sizable reported stake and delegated voting raise governance questions, while conversion blockers limit immediate additional ownership.

The Schedule 13D/A discloses a significant reported holding equal to 13.3% of the outstanding common stock, which is material for investor attention. The filing explicitly notes the Fund holds convertible preferred and pre-funded warrants but is contractually precluded from converting/exercising to exceed a 9.99% ownership cap. The adviser’s sole voting and dispositive authority over the Fund’s securities, coupled with the Fund’s disclaimer of beneficial ownership under Section 13(d), creates a clear allocation of control for voting and disposition while preserving particular reporting positions under the securities rules.

SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 3)

CIDARA THERAPEUTICS, INC.

(Name of Issuer)

Common Stock, $0.0001 par value per share

(Title of Class of Securities)

171757206

(CUSIP Number)

Peter Kolchinsky
RA Capital Management, L.P., 200 Berkeley Street, 18th Floor
Boston, MA, 02116
617.778.2500

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

08/07/2025

(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. 171757206

1

Name of reporting person

RA Capital Management, L.P.

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)

AF

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 0.00
8	Shared Voting Power 3,365,523.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 3,365,523.00

11

Aggregate amount beneficially owned by each reporting person

3,365,523.00

12

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

13

Percent of class represented by amount in Row (11)

13.3 %

14

Type of Reporting Person (See Instructions)

IA, PN

SCHEDULE 13D

CUSIP No. 171757206

1

Name of reporting person

Peter Kolchinsky

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)

AF

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 0.00
8	Shared Voting Power 3,365,523.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 3,365,523.00

11

Aggregate amount beneficially owned by each reporting person

3,365,523.00

12

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

13

Percent of class represented by amount in Row (11)

13.3 %

14

Type of Reporting Person (See Instructions)

HC, IN

SCHEDULE 13D

CUSIP No. 171757206

1

Name of reporting person

Rajeev Shah

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)

AF

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 0.00
8	Shared Voting Power 3,365,523.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 3,365,523.00

11

Aggregate amount beneficially owned by each reporting person

3,365,523.00

12

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

13

Percent of class represented by amount in Row (11)

13.3 %

14

Type of Reporting Person (See Instructions)

HC, IN

SCHEDULE 13D

CUSIP No. 171757206

1

Name of reporting person

RA Capital Healthcare Fund, L.P.

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)

WC

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 0.00
8	Shared Voting Power 3,365,523.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 3,365,523.00

11

Aggregate amount beneficially owned by each reporting person

3,365,523.00

12

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

13

Percent of class represented by amount in Row (11)

13.3 %

14

Type of Reporting Person (See Instructions)

PN

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: CIDARA THERAPEUTICS, INC.
(c)	Address of Issuer's Principal Executive Offices: 6310 NANCY RIDGE DRIVE, SUITE 101, SAN DIEGO, CALIFORNIA , 92121.
Item 1 Comment: Item 1 of the Statement is amended and supplemented as follows: This Amendment No. 3 (this "Amendment No. 3" or this "Schedule 13D/A") amends and supplements the statement on Schedule 13D originally filed with the Securities and Exchange Commission (the "SEC") on July 25, 2024, and amended on November 26, 2024 and June 30, 2025 (as amended, the "Statement") by the Reporting Persons. Unless otherwise defined herein, capitalized terms used in this Amendment No. 3 shall have the meanings ascribed to them in the Statement. Unless amended or supplemented below, the information in the Statement remains unchanged.
Item 2.	Identity and Background
(a)	This Schedule 13D/A is being filed on behalf of RA Capital Management, L.P. ("RA Capital"), Peter Kolchinsky, Rajeev Shah, and RA Capital Healthcare Fund, L.P. (the "Fund"). RA Capital, Dr. Kolchinsky, Mr. Shah and the Fund are collectively referred to herein as the "Reporting Persons." The agreement among the Reporting Persons to file this Schedule 13D/A jointly in accordance with Rule 13d-1(k) of the Securities Exchange Act of 1934, as amended, (the "Act"), is attached hereto as Exhibit 99.1. The Fund directly holds: (i) 3,365,523 shares of common stock; (ii) Series A preferred stock ("Preferred Stock") convertible for up to 6,296,920 shares of common stock; and (iii) pre-funded warrants (the "Pre-Funded Warrants") exercisable for up to 1,286,786 shares of common stock. Each of the Preferred Stock and the Pre-Funded Warrants contains a provision (the "Beneficial Ownership Blockers") which precludes conversion of the Preferred Stock or exercise of the Pre-Funded Warrants to the extent that, following conversion or exercise, the Fund, together with its affiliates and other attribution parties, would own more than 9.99% of the common stock outstanding. The Fund is currently prohibited from converting the Preferred Stock and exercising the Pre-Funded Warrants by virtue of the Beneficial Ownership Blockers. 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 each of the Fund and may be deemed a beneficial owner, for purposes of Section 13(d) of the Act, of any securities of the Issuer held by the Fund. The Fund has delegated to RA Capital the sole power to vote and the sole power to dispose of all securities held in its portfolio, including the shares of the Issuer's common stock reported herein. Because the Fund has divested itself of 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 disclaims 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 13D/A other than for the purpose of determining their obligations under Section 13(d) of the Act, and the filing of this Schedule 13D/A 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)	The address of the principal business office of each of the Reporting Persons is 200 Berkeley Street, 18th Floor, Boston, MA 02116.
(c)	The Fund is a private investment vehicle. RA Capital provides investment management services to the Fund. The principal occupation of each of Dr. Kolchinsky and Mr. Shah is investment management.
(d)	During the last five years, none of the Reporting Persons has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors).
(e)	During the last five years, none of the Reporting Persons has been a party to a civil proceeding of a judicial or administrative body of competent jurisdiction and as a result of such proceeding was or is subject to a judgment, decree of final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.
(f)	See Item 6 of the cover pages.
Item 5.	Interest in Securities of the Issuer
(a)	Rows 11 and 13 of each Reporting Person's cover page to this Schedule 13D/A set forth the aggregate number of shares of common stock and percentages of the shares of common stock beneficially owned by such Reporting Person and are incorporated by reference. The percentage set forth in each row 13 is based upon upon 25,358,051 shares of common stock outstanding as of August 6, 2025, as disclosed in the Issuer's Quarterly Report on Form 10-Q filed with the SEC on August 7, 2025.
(b)	Rows 7 through 10 of each Reporting Person's cover page to this Schedule 13D/A set forth the number of shares of common stock as to which such Reporting Person has the sole or shared power to vote or direct the vote and sole or shared power to dispose or to direct the disposition and are incorporated by reference.
(c)	No transactions with respect to the securities of the Issuer have been effected since the most recent amendment to this Schedule 13D/A by any Reporting Person. The percentage ownership reported in this amendment reflect an increase in the number of outstanding shares of the Issuer.
(d)	No person (other than the Reporting Persons) is known to have the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of, the securities subject to this Statement.
(e)	Not Applicable.
Item 7.	Material to be Filed as Exhibits.
	Exhibit 99.1 Joint Filing Agreement (incorporated by reference to Exhibit 99.1 to the Reporting Persons' Schedule 13D/A filed with the SEC on June 30, 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.

RA Capital Management, L.P.

Signature:	/s/ Peter Kolchinsky
Name/Title:	By Peter Kolchinsky, Authorized Signatory
Date:	08/11/2025

Peter Kolchinsky

Signature:	/s/ Peter Kolchinsky
Name/Title:	Peter Kolchinsky
Date:	08/11/2025

Rajeev Shah

Signature:	/s/ Rajeev Shah
Name/Title:	Rajeev Shah
Date:	08/11/2025

RA Capital Healthcare Fund, L.P.

Signature:	/s/ Peter Kolchinsky
Name/Title:	By RA Capital Healthcare Fund GP, LLC, its General Partner, By Peter Kolchinsky, Manager
Date:	08/11/2025

FAQ

How many Cidara Therapeutics (CDTX) shares does RA Capital report owning?

The Reporting Persons state ownership of 3,365,523 shares of common stock, equal to 13.3% of 25,358,051 shares outstanding.

Does RA Capital or its fund hold convertible securities in CDTX?

Yes. The Fund holds Series A preferred stock convertible into up to 6,296,920 common shares and pre-funded warrants exercisable for up to 1,286,786 common shares.

Can the Fund currently convert the preferred stock or exercise the pre-funded warrants?

No. Conversion and exercise are currently restricted by Beneficial Ownership Blockers that prevent the Fund from owning more than 9.99% of the common stock.

Who has the voting and dispositive power over the Fund’s reported CDTX securities?

RA Capital, as investment adviser, has been delegated the sole power to vote and to dispose of the Fund’s securities.

Have any transactions been reported since the last Schedule 13D/A amendment?

The filing states no transactions with respect to the issuer’s securities have been effected since the most recent amendment.