daptomycin

CHEBI:600103 ·resolve ·ANTIBACTERIAL ·EXACT SEEDED

A polypeptide comprising N-decanoyltryptophan, asparagine, aspartic acid, threonine, glycine, ornithine, aspartic acid, D-alanine, aspartic acid, glycine, D-serine, threo-3-methylglutamic acid and 3-anthraniloylalanine (also known as kynurinine) coupled in sequence and lactonised by condensation of the carboxylic acid group of the 3-anthraniloylalanine with the alcohol group of the threonine residue. — ChEBI

Classification

nonribosomal peptide antibioticsARO:3009657

Strictly broader compounds or drug classes this molecule belongs to.

• Label unavailable CHEBI:24533
• Label unavailable CHEBI:25061
• Label unavailable CHEBI:25106
• Label unavailable CHEBI:46895
• Label unavailable CHEBI:51026
• nonribosomal peptide antibiotics ARO:3009657

Chemical structure

SMILES

CCCCCCCCCC(=O)N[C@@H](Cc1cnc2ccccc12)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H]1C(=O)NCC(=O)N[C@@H](CCCN)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@H](C)C(=O)N[C@@H](CC(=O)O)C(=O)NCC(=O)N[C@H](CO)C(=O)N[C@@H]([C@H](C)CC(=O)O)C(=O)N[C@@H](CC(=O)c2ccccc2N)C(=O)O[C@@H]1C

InChI

InChI=1S/C72H101N17O26/c1-5-6-7-8-9-10-11-22-53(93)81-44(25-38-31-76-42-20-15-13-17-39(38)42)66(108)84-45(27-52(75)92)67(109)86-48(30-59(102)103)68(110)89-61-37(4)115-72(114)49(26-51(91)40-18-12-14-19-41(40)74)87-71(113)60(35(2)24-56(96)97)88-69(111)50(34-90)82-55(95)32-77-63(105)46(28-57(98)99)83-62(104)36(3)79-65(107)47(29-58(100)101)85-64(106)43(21-16-23-73)80-54(94)33-78-70(61)112/h12-15,17-20,31,35-37,43-50,60-61,76,90H,5-11,16,21-30,32-34,73-74H2,1-4H3,(H2,75,92)(H,77,105)(H,78,112)(H,79,107)(H,80,94)(H,81,93)(H,82,95)(H,83,104)(H,84,108)(H,85,106)(H,86,109)(H,87,113)(H,88,111)(H,89,110)(H,96,97)(H,98,99)(H,100,101)(H,102,103)/t35-,36-,37-,43+,44+,45+,46+,47+,48+,49+,50-,60+,61+/m1/s1

Also called

• Cidecin (BRAND_NAME)— chebi
• Cubicin (BRAND_NAME)— chebi
• daptomicina (INN)— chebi
• daptomycine (INN)— chebi
• daptomycinum (INN)— chebi
• N-decanoyl-L-tryptophyl-L-asparaginyl-N-[(3S,6S,9R,15S,18R,21S,24S,30S,31R)-3-[2-(2-aminophenyl)-2-oxoethyl]-24-(3-aminopropyl)-15,21-bis(carboxymethyl)-6-[(2R)-1-carboxypropan-2-yl]-9-(hydroxymethyl)-18,31-dimethyl-2,5,8,11,14,17,20,23,26,29-decaoxo-1-oxa-4,7,10,13,16,19,22,25,28-nonaazacyclohentriacontan-30-yl]-L-α-asparagine (EXACT_SYNONYM)— chebi
• Daptomycin (EXACT_SYNONYM)— chebi
• LY 146032 (EXACT_SYNONYM)— chebi
• N-decanoyl-L-tryptophyl-L-asparaginyl-L-aspartyl-L-threonylglycyl-L-ornithyl-L-aspartyl-D-alanyl-L-aspartylglycyl-D-seryl-threo-3-methyl-L-glutamyl-3-anthraniloyl-L-alanine 1.13-3.4-lactone (EXACT_SYNONYM)— chebi
• N-decanoyl-L-tryptophyl-L-asparaginyl-L-aspartyl-L-threonylglycyl-L-ornithyl-L-aspartyl-D-alanyl-L-aspartylglycyl-D-seryl-threo-3-methyl-L-glutamyl-3-anthraniloyl-L-alanine ε1-lactone (EXACT_SYNONYM)— chebi
• Daptomicina (EXACT_SYNONYM)— aro
• Daptomycine (EXACT_SYNONYM)— aro
• Daptomycinum (EXACT_SYNONYM)— aro
• Deptomycin (EXACT_SYNONYM)— aro

Cross-references

Identifiers for this same structure in other resources. An accession that lands on two different structures in this corpus is withheld from both rather than shown here, since it names at most one of them.

• daptomycinARO:0000068
• cas:103060-53-3
• kegg.compound:C12013
• pubchem.compound:16134395

Drug registries

Identifiers that name a drug rather than a structure. One of these can cover a parent compound, its salts and its stereoisomers, which this corpus keeps as separate records, so it is not an equivalence of structure.

• drugbank:DB00080
• kegg.drug:D01080

Patents and articles

Documents about this compound. A patent covers a class and an article covers a topic; neither identifies a structure.

• wikipedia.en:Daptomycin

Activity roles

Every antimicrobial role a source asserts for this compound — the unreduced evidence behind its antimicrobial_class.

• calcium-dependent antibiotics CHEBI:140190
• antimicrobial agent CHEBI:33281
• antibacterial drug CHEBI:36047

Source concepts

Every upstream concept that resolved to this record. The merge is the product: this is what shows ChEBI and CARD are describing the same structure.

Molecular targets

The molecular entity or process this compound acts on. Each target carries evidence — this is a mechanistic claim, not a classification.

Daptomycin sensitive cardiolipin synthetase PROTEIN SUSCEPTIBILITY_DETERMINANT

ARO:3003275

CARD/ARO database assertion; target organism, strain, and assay are not specified. ARO cites cls mutations conferring daptomycin resistance; this does not prove direct binding. Evidence status: DATABASE_ASSERTION_ONLY. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

• ARO:3003275 (CARD/ARO asserts targeted_by_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)

daptomycin sensitive beta-subunit of RNA polymerase (rpoB) BIOLOGICAL_PROCESS DOWNSTREAM_AFFECTED_PROCESS

ARO:3003278

CARD/ARO database assertion; target organism, strain, and assay are not specified. ARO describes RNA-synthesis failure downstream of daptomycin membrane depolarization, not rpoB binding. Evidence status: DATABASE_ASSERTION_ONLY. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

• ARO:3003278 (CARD/ARO asserts targeted_by_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)

antibiotic sensitive mprF PROTEIN SUSCEPTIBILITY_DETERMINANT

ARO:3003280

CARD/ARO database assertion; target organism, strain, and assay are not specified. ARO describes mprF membrane-charge effects and resistance mutations, not direct binding. Evidence status: DATABASE_ASSERTION_ONLY. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

• ARO:3003280 (CARD/ARO asserts targeted_by_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)

antibiotic sensitive pgsA PROTEIN SUSCEPTIBILITY_DETERMINANT

ARO:3003281

CARD/ARO database assertion; target organism, strain, and assay are not specified. ARO associates pgsA with membrane phospholipid state; direct daptomycin binding is not established. Evidence status: DATABASE_ASSERTION_ONLY. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

• ARO:3003281 (CARD/ARO asserts targeted_by_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)

phosphatidylglycerol-rich bacterial membrane MEMBRANE DIRECT_BINDING_TARGET

Biophysical and cellular study of the calcium-dependent daptomycin- phosphatidylglycerol complex and selective uptake into bacterial membranes; no single organism or strain is generalized from the membrane models. Evidence status: PRIMARY_EVIDENCE. Source: CURATOR 2026-08-31 (retrieved 2026-08-31).

• PMID:40455071 (Primary evidence for stable phosphatidylglycerol complex formation and selective bacterial-membrane uptake.)

Activity spectrum

Measured or curated activity against specific taxa. A number without a method is not an observation — every row here carries an assay.

19 observations · Browse all observations · Complete record (JSON.gz)

Resistance mechanisms

35 source-backed resistance determinants or associations, with ARO grounding where reported. Grouped by reported mechanism type.

Causal graphs

Evidence-backed mechanism graphs: how the compound reaches its target, what the target does, and how the effect propagates to growth inhibition or death.

Daptomycin targets phosphatidylglycerol-rich bacterial membranes MECHANISTIC

Daptomycin forms a calcium-dependent complex with phosphatidylglycerol-rich bacterial membranes, enabling selective membrane insertion and membrane-potential dissipation.

Curation history

1. SEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources

   Seeded from data/raw/ inventories (ARO, CHEBI)

2. RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources

   Re-seeded from updated data/raw/ inventories

3. RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources

   Re-seeded from updated data/raw/ inventories

4. RESEEDED_FROM_SOURCES 2026-08-31 · seed_from_sources

   Re-seeded from updated data/raw/ inventories

5. CURATED_CAUSAL_GRAPH 2026-09-04 · codex · LLM-assisted

   Added a PMID-supported causal graph for calcium-dependent daptomycin-phosphatidylglycerol membrane targeting.

6. RESEEDED_FROM_SOURCES 2026-09-10 · seed_from_sources

   Re-seeded from updated data/raw/ inventories

7. CURATED_RESISTANT_TAXA 2026-09-12 · codex · LLM-assisted

   Added 19 CDC Sentinel Surveillance daptomycin-resistant Enterococcus faecalis/faecium isolate MIC observations from Gargis et al. 2022.

8. STRUCTURED_ACTIVITY_BIOSAMPLE_ACCESSIONS 2026-09-26 · codex · LLM-assisted

   Structured BioSample accessions on 19 activity_spectrum observation(s) where evidence notes already named exactly one accession.

9. RESEEDED_FROM_SOURCES 2026-10-16 · seed_from_sources

   Re-seeded; changed: resistance_mechanisms (CARD). Upstream retrieval date 2026-08-30, unchanged.

10. RESEEDED_FROM_SOURCES 2026-10-16 · seed_from_sources

    Re-seeded; changed: resistance_mechanisms (CARD). Upstream retrieval date 2026-08-30, unchanged.

Provenance

Seeded by scripts/seed_from_sources.py from the committed inventories in data/raw/. View the record (YAML).

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