Is Retatrutide a Peptide or a Protein? The 40-Amino-Acid Line Behind Lilly v. Kennedy
US law calls a polymer a protein only when it is greater than 40 amino acids. Retatrutide is counted as 39, 40 plus 1 or 41. The appeal hearing is set for 24 September 2026.

A post in r/Retatrutide from 22 April 2026, with 418 points, puts the question people ask into two sentences: "The FDA said retatrutide doesn't meet that bar. Lilly says it does, counting 41." Under US regulations, an amino acid polymer is a protein, and therefore a biological product, only when its size is greater than 40 amino acids. Retatrutide, Lilly's investigational triple agonist at the GLP-1, GIP and glucagon receptors, sits on that line, with three counts of the same molecule: 39 backbone residues in the nomenclature of the World Health Organization (WHO), 40 alpha amino acids plus 1 non-alpha amino acid in the count of the US Food and Drug Administration (FDA), and 41 in Lilly's cumulative count. The US Court of Appeals for the Seventh Circuit is scheduled to hear argument on 24 September 2026. This article describes that US dispute for its chemistry and its record as of 23 September 2026; it is not legal advice and not a statement about any product.
TL;DR: one molecule, three counts, one line at 40
- The rule: since 23 March 2020, 21 CFR 600.3(h)(6) defines a protein as an alpha amino acid polymer with a specific, defined sequence that is greater than 40 amino acids in size.
- Three counts: 39 is the WHO backbone; 40 alpha plus 1 non-alpha amino acid is FDA's count (letter of 18 March 2024); 41 is Lilly's cumulative count, which adds the gamma-glutamate and the ADO unit of the lysine 17 side chain.
- The district court held that the regulation requires at least 41 alpha amino acids and upheld FDA on that point, but set aside FDA's decision that retatrutide is not analogous to a protein and remanded that question to the agency (Amended Order, 3 October 2025; Final Judgment, 16 December 2025).
- The appeal: the Seventh Circuit is scheduled to hear argument on 24 September 2026 at 9:30 a.m. in Chicago, 15 minutes per side.
- Why it matters: the label decides between a biologics license application (BLA) and a new drug application (NDA), and between 12 and 5 years of statutory exclusivity.
Research use only
Retatrutide is sold here as a laboratory research material, not as a medicine, and not for administration to a person or animal. This article describes a US classification dispute between Eli Lilly and FDA; it makes no claim about the legal status of any product, including ours, and contains no dosing, use or purchasing information. Tirzepatide and insulin appear only as reference molecules.
Retatrutide (LY3437943) is a synthetic 39-amino-acid peptide that acts on three receptors at once: GLP-1, GIP and glucagon. Supplied as a lyophilized powder for in-vitro research, with a batch-specific third-party certificate of analysis.
GIP/GLP-1/glucagon agonists and metabolic pathways
Where US law draws the line
The statute, 42 U.S.C. 262(i)(1) in the Public Health Service Act, begins: "The term 'biological product' means a virus, therapeutic serum, toxin, antitoxin, vaccine, blood, blood component or derivative, allergenic product, protein, or analogous product, ..." Two terms in that list carry this case: protein and analogous product.
The Biologics Price Competition and Innovation Act of 2009 had put an exception into the definition: "protein (except any chemically synthesized polypeptide)". A later FDA memo, as described by the district court, read protein as greater than 40 amino acids and defined a chemically synthesized polypeptide in two parts: "(a) made entirely by chemical synthesis; and (b) less than 100 amino acids in size". The 2018 proposed rule set the category at greater than 40 but less than 100 amino acids. On 20 December 2019, Pub. L. 116-94, § 605 struck the exception.
FDA's final rule of 21 February 2020 (85 FR 10057) took effect on 23 March 2020. With the exception gone, FDA did not finalize its interpretation of chemically synthesized polypeptide and gave this reason: "because it is no longer necessary". Nor did the rule define analogous products; Response 8 describes such a definition as outside the scope of the rulemaking. The protein definition is codified in 21 CFR 600.3(h)(6) and reads in full: "A protein is any alpha amino acid polymer with a specific, defined sequence that is greater than 40 amino acids in size. When two or more amino acid chains in an amino acid polymer are associated with each other in a manner that occurs in nature, the size of the amino acid polymer for purposes of this paragraph (h)(6) will be based on the total number of amino acids in those chains, and will not be limited to the number of amino acids in a contiguous sequence." The word peptide does not appear in section 600.3 as retrieved on 23 September 2026.
FDA did not claim that science draws the line at 40; Response 3 of the rule reads: "While we agree that there may not be clear scientific consensus for a particular number of amino acids to use when distinguishing between the terms 'protein' and 'peptide,' there is strong support in scientific literature for distinguishing between types of amino acid polymers based on the number of amino acids they contain." FDA also rejected folding as a criterion, with this reason in Response 1: "relying on a factor such as 'folding' would not provide regulatory certainty".
The second sentence of the definition matters for molecules built from more than one chain, and FDA's worked example is insulin. Response 4 states: "insulin is an alpha amino acid polymer with a specific, defined sequence consisting of 2 amino acid chain subunits with 21 amino acids and 30 amino acids, respectively. ... we conclude that insulin is an alpha amino acid polymer with a specific, defined sequence of 51 amino acids." Neither chain alone exceeds 40; together, 21 + 30 = 51. Lilly's request, quoted below, describes a second, associated chain in retatrutide.
Counting retatrutide: 39, 40 plus 1, or 41
Proposed INN List 128 (WHO Drug Information Vol. 36 No. 4, published 20 January 2023) lists the molecular formula C221H342N46O68, the CAS number 2381089-83-2 and this sequence of 39 one-letter codes: "YAQGTFTSDY SILLDKKAQA AFIEYLLEGG PSSGAPPPS". The modified residues it names are Aib (2-methyl-alanine) at positions 2 and 20, 2-methyl-L-leucine at 13, a lysine at 17 with a substituent on its N6 nitrogen, and the C-terminal serinamide (L-Ser-NH2) at 39. Recommended INN List 90 (WHO Drug Information Vol. 37 No. 3, 2023) spells out the lysine 17 substituent in the IUPAC name: N6-{2-[2-(2-{[N-(19-carboxynonadecanoyl)-L-γ-glutamyl]amino}ethoxy)ethoxy]acetyl}. It contains three units: a gamma-glutamate, linked through its gamma carboxyl in the side chain; ADO (8-amino-3,6-dioxaoctanoic acid); and a C20 diacid, 19-carboxynonadecanoyl. Our guide to reading a peptide name explains such names, Aib and C-terminal amidation.
- Who
- WHO nomenclature
- What is counted
- The backbone: tyrosine at position 1 to the serinamide at position 39
- Source
- WHO Proposed INN List 128, 20 January 2023
- Who
- FDA
- What is counted
- Alpha amino acids, including the gamma-glutamate of the side chain; ADO counted as a non-alpha amino acid
- Source
- FDA letter of designation, 18 March 2024, as quoted in Doc. 48
- Who
- Lilly
- What is counted
- All amino acids: the 39 backbone residues plus the gamma-glutamate and ADO (39 + 2 = 41)
- Source
- Lilly's request for designation, as quoted in Doc. 48
Lilly's request for designation (9 November 2023, superseded on 29 January 2024), as quoted by the district court, reads: "Retatrutide is an alpha amino acid polymer that contains a specific, defined sequence of 41 amino acids cumulatively, comprising a backbone of 39 alpha amino acids and a second (associated) chain of one residue each of gamma-glutamate and 8-amino-3,6-dioxaoctanoic acid (ADO)." On ADO, Lilly added: "ADO has additional carbons (and oxygens) between the amino group and the carboxyl group ... and it is more complex than many alpha amino acids".
The Amended Order summarizes FDA's letter of designation of 18 March 2024: "At most, says FDA, retatrutide contains 40 alpha amino acids and 1 non-alpha amino acid. ... Because proteins must have more than 40 alpha amino acids, retatrutide does not count." FDA grounded the alpha requirement in biochemistry, in words the court quotes: "[a]lthough more than 300 amino acids exist in nature, proteins of humans are synthesized almost exclusively from 20 alpha amino acids."
So the three numbers answer three questions about one structure. Only the backbone is represented in the WHO sequence string. FDA counts alpha amino acids wherever they sit, which brings in the side-chain gamma-glutamate and leaves out ADO as non-alpha. Lilly counts all amino acids across what it calls a backbone and an associated chain. In the quoted documents both sides describe the same components; they differ on which ones the regulation counts. How a 39-residue backbone is assembled is covered in our article on SPPS and LPPS.
What the district court decided
The case is Eli Lilly and Company v. Kennedy, No. 1:24-cv-01503-TWP-KMB, in the US District Court for the Southern District of Indiana, before Judge Tanya Walton Pratt. Lilly filed its complaint on 3 September 2024, and the court heard argument on cross-motions for summary judgment on 7 August 2025. An order of 30 September 2025 (Doc. 47) was replaced on 3 October 2025 by the Amended Order on Cross-Motions for Summary Judgment (Doc. 48); this article quotes only the Amended Order and the Final Judgment.
On the count, the court upheld FDA. In the court's words: "At bottom, the regulation unambiguously requires that proteins contain at least forty-one alpha amino acids. Because retatrutide contains forty alpha amino acids at most, the agency did not violate its own regulations and its decision not to designate retatrutide as a protein was not arbitrary and capricious."
On Lilly's alternative argument, that retatrutide is at least analogous to a protein, the court ruled against FDA: "FDA's 'bright line' approach flouts the statutory text and sidesteps congressional intent." And: "By requiring 'analogous' products to meet each and every requirement for a 'protein,' FDA effectively reads 'analogous product' out of the statute." Its conclusion on the point: "Because the agency's decision that retatrutide is not at least analogous to a protein was not in accordance with the law, it was arbitrary and capricious and must be set aside."
The Final Judgment (Doc. 54) of 16 December 2025 sets out the result: "Consistent with the Court's Amended Order on Cross-Motions for Summary Judgment, the Court hereby VACATES the agency's designation decision and REMANDS to the agency for further proceedings on Plaintiff's 'analogous' products claim."
The Amended Order decided two of Lilly's three claims; in its own words: "this Order addresses only claims two and three". The first claim, that the refusal exceeded FDA's statutory authority, was left open.
The appeal: what the Seventh Circuit hears on 24 September
Lilly filed its notice of appeal on 12 February 2026. The Seventh Circuit docketed it on 17 February 2026 as No. 26-1301, Eli Lilly and Company v. Robert Kennedy, Jr.
- Filing
- Appellant's brief (Lilly)
- Appeals docket
- Doc. 12
- Filing
- Appellees' brief (government), entered 18 May 2026
- Appeals docket
- Doc. 23
- Filing
- Amicus brief, Outsourcing Facilities Association
- Appeals docket
- Doc. 27
- Filing
- Appellant's reply (Lilly)
- Appeals docket
- Doc. 31
- Filing
- Order setting oral argument
- Appeals docket
- Doc. 36
- Filing
- FDA letter under Circuit Rule 28(e)
- Appeals docket
- Doc. 41
The order of 27 July 2026 reads: "Argument set for Thursday, September 24,2026, at 9:30 a.m. in the Main Courtroom, Room 2721, of the United States Court of Appeals for the Seventh Circuit, 219 S. Dearborn Street, Chicago, Illinois. Each side limited to 15 minutes."
Lilly's opening brief states three questions:
- "Whether Lilly's product retatrutide, which is composed of 41 amino acids, satisfies a regulatory requirement that a 'protein' must be 'greater than 40 amino acids in size,' where size is 'based on the total number of amino acids.' ..."
- "Whether the district court erred in remanding to the agency despite the mandatory 60-day deadline for FDA designation decisions, 21 U.S.C. § 360bbb-2(b), and the automatic take-effect provision ..."
- "Whether this Court should order FDA to treat Lilly's request for designation has [sic] having been granted, given that more than 60 days have passed since its designation decision was vacated, and the agency still has not issued any decision."
Questions two and three rest on the designation procedure in 21 U.S.C. 360bbb-2, whose fallback rule the Amended Order describes: "If the Secretary fails to provide a statement within the sixty-day period, then the recommendation of the product's sponsor will be considered the final determination". Lilly's reply describes the government's answer as follows: "the government argues that once FDA issues any designation decision, the FDCA's automatic take-effect provision becomes irrelevant even if a court vacates that decision". That is Lilly's summary, not the government's wording.
In the same reply of 5 June 2026, Lilly made this statement about the remand: "almost six months have now passed since the district court's decision, with no fda action in sight." It is a party statement in a brief.
FDA's letter of 21 September 2026 cites Franco v. Chobani, 184 F.4th 599 (7th Cir. 2026), as additional authority and states: "FDA's understanding of the protein definition is an 'especially informative' tool of regulatory interpretation."
The amicus brief of the Outsourcing Facilities Association contains these two lines: "Lilly's Demand for Immediate Designation Is Not Properly Before the Court and Fails on the Merits" and "Lilly's money grab should not be sanctioned by this Court." Both are amicus statements, not findings of any court.
Status as of 23 September 2026: no FDA decision on the remanded analogous-product claim appears in the docket entries we checked; the newest entries are FDA's letter of 21 September 2026 on the appeals docket and one of 3 March 2026 on the district court docket.
Why the label matters
A biological product is licensed through a BLA under section 351 of the Public Health Service Act (PHS Act); a drug is approved through an NDA under section 505 of the Federal Food, Drug, and Cosmetic Act (FD&C Act). For biological products, 42 U.S.C. 262(k)(7) provides: "Approval of an application under this subsection may not be made effective by the Secretary until the date that is 12 years after the date on which the reference product was first licensed under subsection (a)." The same subsection bars the submission of such an application until 4 years after that first licensure. For drugs, 21 U.S.C. 355(c)(3)(E)(ii) sets a five-year period for a new chemical entity; its operative words are: "before the expiration of five years from the date of the approval of the application".
On 23 March 2020, the day the protein definition took effect, approved NDAs for biological products changed status. FDA's notice at 85 FR 12930 states: "On March 23, 2020, an approved application for a biological product under section 505 of the FD&C Act shall be deemed to be a license for the biological product under section 351 of the PHS Act." FDA's list of the transitioned applications, updated on 2 April 2020, includes insulin lispro (Humalog, application 020563).
FDA's questions-and-answers page on compounding (content current as of 16 September 2025) states the legal status of biological products in these words: "Biological products are not eligible for the exemptions for compounded drugs under sections 503A and 503B of the FD&C Act."
Lilly's Form 8-K exhibit on second-quarter 2026 results, dated 5 August 2026, describes the plan for retatrutide in these words: "with plans to submit a Biologics License Application to the U.S. FDA in the first quarter of 2027." The approval timeline is covered in our article on retatrutide's approval status.
Other molecules near the line
The table records what each source states and applies no party's counting method to the other molecules.
- Size stated in the source
- 2 chains of 21 and 30 amino acids, 51 in total
- US application type
- Approved under NDAs; deemed BLAs on 23 March 2020 (for example Humalog, 020563)
- Source
- 85 FR 10057; FDA transition list, 2 April 2020
- Size stated in the source
- 39, per the 2022 label
- US application type
- NDA 215866 (Mounjaro)
- Source
- Mounjaro label, 2022
- Size stated in the source
- 39 (WHO backbone), 40 + 1 (FDA), 41 (Lilly), by count
- US application type
- BLA submission planned for the first quarter of 2027
- Source
- WHO Proposed INN List 128; Doc. 48; Lilly Form 8-K, 5 August 2026
The 2022 Mounjaro label describes tirzepatide in one sentence: "It is a 39-amino-acid modified peptide based on the GIP sequence."
What the community asks
What the community reports
Demand, not evidence. In our Reddit corpus (212,225 posts, 1 August 2025 to 16 September 2026, posts only, no comments), the dispute appears in posts such as these two. A post in r/Retatrutide from 22 April 2026 (418 points) reads: "The FDA said retatrutide doesn't meet that bar. Lilly says it does, counting 41." A post in r/Biohacking from 26 August 2026 (157 points, 230 comments) reads: "US law draws a bright line at 40 amino acids (for scale, tirzepatide sits at 39, one under the line)."
Both posts show what readers discuss; the counts in this article come from the documents cited.
What to watch
- 24 September 2026: the Seventh Circuit is scheduled to hear argument in No. 26-1301. A decision date is not known.
- The remand at FDA: the analogous-product question has been with the agency since the Final Judgment of 16 December 2025; as of 23 September 2026, no FDA decision on it appears in the docket entries we checked.
- First quarter of 2027: Lilly's stated plan to submit a BLA for retatrutide, per its Form 8-K of 5 August 2026.
These are dated facts, not a forecast. The receptor mechanism of retatrutide is covered in our article on GLP-1, GIP and glucagon triple agonists.
FAQ
Sources
- Reddit corpus, our own extraction: 212,225 posts, 1 August 2025 to 16 September 2026, posts only, no comments; posts cited by subreddit, date and score, not linked.
- Code of Federal Regulations, 21 CFR 600.3(h)(6), eCFR, up to date as of 21 September 2026. https://www.ecfr.gov/current/title-21/chapter-I/subchapter-F/part-600/subpart-A/section-600.3
- World Health Organization. Proposed INN List 128, WHO Drug Information Vol. 36 No. 4, published 20 January 2023 (retatrutide). https://cdn.who.int/media/docs/default-source/international-nonproprietary-names-(inn)/pl128.pdf
- Eli Lilly and Company v. Kennedy, U.S. District Court for the Southern District of Indiana, No. 1:24-cv-01503-TWP-KMB, Amended Order on Cross-Motions for Summary Judgment (Doc. 48), 3 October 2025. https://www.govinfo.gov/content/pkg/USCOURTS-insd-1_24-cv-01503/pdf/USCOURTS-insd-1_24-cv-01503-1.pdf
- Eli Lilly and Company v. Robert Kennedy, Jr., U.S. Court of Appeals for the Seventh Circuit, No. 26-1301: docket, Appellant's Brief (Doc. 12, 1 April 2026), amicus brief of the Outsourcing Facilities Association (Doc. 27), Appellant's Reply (Doc. 31, 5 June 2026), order setting argument (Doc. 36, 27 July 2026), FDA letter under Circuit Rule 28(e) (Doc. 41, 21 September 2026). https://www.courtlistener.com/docket/73173235/eli-lilly-and-company-v-robert-kennedy-jr/
- Eli Lilly and Company v. Kennedy, S.D. Ind. No. 1:24-cv-01503-TWP-KMB, Final Judgment (Doc. 54), 16 December 2025. https://storage.courtlistener.com/recap/gov.uscourts.insd.216702/gov.uscourts.insd.216702.54.0.pdf
- 42 U.S.C. 262 (Public Health Service Act section 351), including subsections (i)(1) and (k)(7), Cornell Legal Information Institute. https://www.law.cornell.edu/uscode/text/42/262
- 21 U.S.C. 355(c)(3)(E)(ii), Cornell Legal Information Institute. https://www.law.cornell.edu/uscode/text/21/355
- FDA. Definition of the Term "Biological Product". Final rule, 85 FR 10057, 21 February 2020, effective 23 March 2020. https://www.federalregister.gov/documents/2020/02/21/2020-03505/definition-of-the-term-biological-product
- World Health Organization. Recommended INN List 90, WHO Drug Information Vol. 37 No. 3, 2023 (retatrutide). https://cdn.who.int/media/docs/default-source/international-nonproprietary-names-(inn)/rl90.pdf
- FDA. Notice on the transition of biological products approved under section 505 ("deemed to be a license"), 85 FR 12930, FR Doc. 2020-04537, 5 March 2020. https://www.federalregister.gov/d/2020-04537
- FDA. List of approved NDAs for biological products that were deemed to be BLAs on 23 March 2020 (updated 2 April 2020). https://www.fda.gov/media/119229/download
- FDA. Compounding and the FDA: Questions and Answers, content current as of 16 September 2025. https://www.fda.gov/drugs/human-drug-compounding/compounding-and-fda-questions-and-answers
- Eli Lilly and Company. Form 8-K, exhibit on second-quarter 2026 results, 5 August 2026. https://www.sec.gov/Archives/edgar/data/0000059478/000005947826000077/q226lillysalesandearningsp.htm
- Mounjaro (tirzepatide) prescribing information, initial approval label 2022, NDA 215866. https://www.accessdata.fda.gov/drugsatfda_docs/label/2022/215866s000lbl.pdf
Research use only. Retatrutide is supplied for laboratory research only, not as a medicine, and not for administration to a person or animal. Tirzepatide and insulin are named in this article only as reference molecules; PeptidesDirect does not sell them. This article describes a US legal dispute as of 23 September 2026 and is not legal advice.
Research context for English-speaking buyers
Most of our English-speaking customers ship to the UK, Ireland, Malta or other English-as-second-language EU territories. The regulatory picture differs per country.
- Relevant authorities
- MHRA (UK, post-Brexit), HPRA (Ireland, EU-aligned), FDA Section 503A bulks list (US, restricted Cat 2 status of several peptides as of 2026)
- Customs and VAT
- EU shipments include VAT, the rate depends on the destination country; UK shipments after Brexit are now extra-EU and may attract UK VAT plus a handling fee at import
- Typical shipping window
- EU 2-4 working days, UK 4-7 working days, other international 7-14 working days, depending on customs
Research-grade peptides shipped from our EU warehouse are sold for laboratory use only and are not authorised for human or veterinary therapeutic application in any of the destination jurisdictions. US customers should be aware that the FDA Section 503A bulks list classification (and the April 2026 reclassification of twelve compounds) only governs compounding pharmacies, not direct-to-researcher imports for non-clinical work. UK buyers should declare the consignment on import and may be asked for a research justification by HMRC. We provide a CoA per batch identified by colour code rather than serial number; customs sometimes asks for this document when clearing the parcel.