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
Machine-generated and unreviewed. Identity, structure and
cross-references come straight from ChEBI's and CARD's own data; no curator has
signed off on this record yet.
Classification
nonribosomal peptide antibioticsARO:3009657
Strictly broader compounds or drug classes this molecule belongs to.
Chemical structure
Computed structure properties
| Molecular formula | C72H101N17O26 |
|---|
| Charge | 0 |
|---|
| Average mass | 1620.693 Da |
|---|
| Monoisotopic mass | 1619.71037 Da |
|---|
| Source | ChEBI |
|---|
| InChIKey | DOAKLVKFURWEDJ-RWDRXURGSA-N |
|---|
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
Equivalent identifiers for this same structure in other resources.
Activity roles
Every antimicrobial role a source asserts for this compound — the
unreduced evidence behind its antimicrobial_class.
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.
Upstream concepts merged into this record
| Source | Native ID | Label | Minted CURIE | Version |
|---|
| ARO |
ARO:0000068 |
daptomycin |
antibioticmech:aro-310dde21ed |
2026-08-30 |
| CHEBI |
CHEBI:600103 |
daptomycin |
antibioticmech:chebi-f00562bff4 |
2026-08-30 |
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.)
Resistance mechanisms
35 known routes by which microbes
resist this compound, grounded in ARO where CARD models them. Grouped by mechanism
type — expand a group to see its determinants.
ANTIBIOTIC_TARGET_ALTERATION 34
ANTIBIOTIC_TARGET_ALTERATION
| Determinant | ARO ID | Organism | Gene families | Evidence |
|---|
| Bacillus subtilis pgsA with mutation conferring resistance to daptomycin |
ARO:3003788 |
not organism-specific |
— |
- ARO:3003788 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Enterococcus faecalis YvlB with mutation conferring daptomycin resistance |
ARO:3003815 |
not organism-specific |
— |
- ARO:3003815 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Enterococcus faecalis YybT with mutation conferring daptomycin resistance |
ARO:3003797 |
not organism-specific |
— |
- ARO:3003797 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Enterococcus faecalis cls with mutation conferring resistance to daptomycin |
ARO:3003760 |
not organism-specific |
— |
- ARO:3003760 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Enterococcus faecalis drmA with mutation conferring daptomycin resistance |
ARO:3003813 |
not organism-specific |
— |
- ARO:3003813 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Enterococcus faecalis gdpD with mutation conferring daptomycin resistance |
ARO:3003800 |
not organism-specific |
— |
- ARO:3003800 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Enterococcus faecalis gshF with mutation conferring daptomycin resistance |
ARO:3003805 |
not organism-specific |
— |
- ARO:3003805 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Enterococcus faecalis liaF mutant conferring daptomycin resistance |
ARO:3003077 |
not organism-specific |
— |
- ARO:3003077 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Enterococcus faecalis liaR mutant conferring daptomycin resistance |
ARO:3003792 |
not organism-specific |
— |
- ARO:3003792 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Enterococcus faecalis liaS mutant conferring daptomycin resistance |
ARO:3003791 |
not organism-specific |
— |
- ARO:3003791 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Enterococcus faecium cls conferring resistance to daptomycin |
ARO:3003092 |
not organism-specific |
— |
- ARO:3003092 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Enterococcus faecium liaF mutant conferring daptomycin resistance |
ARO:3003790 |
not organism-specific |
— |
- ARO:3003790 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Enterococcus faecium liaR mutant conferring daptomycin resistance |
ARO:3003078 |
not organism-specific |
— |
- ARO:3003078 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Enterococcus faecium liaS mutant conferring daptomycin resistance |
ARO:3003079 |
not organism-specific |
— |
- ARO:3003079 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Staphylococcus aureus agrA with mutation conferring resistance to daptomycin |
ARO:3003803 |
not organism-specific |
— |
- ARO:3003803 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Staphylococcus aureus cls conferring resistance to daptomycin |
ARO:3003074 |
not organism-specific |
— |
- ARO:3003074 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Staphylococcus aureus mprF with mutation conferring resistance to daptomycin |
ARO:3003319 |
not organism-specific |
— |
- ARO:3003319 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Staphylococcus aureus pgsA mutations conferring resistance to daptomycin |
ARO:3003323 |
not organism-specific |
— |
- ARO:3003323 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Staphylococcus aureus rpoB mutants conferring resistance to daptomycin |
ARO:3003287 |
not organism-specific |
— |
- ARO:3003287 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Staphylococcus aureus rpoC conferring resistance to daptomycin |
ARO:3003291 |
not organism-specific |
— |
- ARO:3003291 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Staphylococcus aureus walK with mutation conferring resistance to daptomycin |
ARO:3003794 |
not organism-specific |
— |
- ARO:3003794 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| Streptococcus mitis CdsA with mutation conferring daptomycin resistance |
ARO:3004097 |
not organism-specific |
— |
- ARO:3004097 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| daptomycin resistant CdsA |
ARO:3004096 |
not organism-specific |
— |
- ARO:3004096 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| daptomycin resistant YvlB |
ARO:3003816 |
not organism-specific |
— |
- ARO:3003816 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| daptomycin resistant YybT |
ARO:3003798 |
not organism-specific |
— |
- ARO:3003798 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| daptomycin resistant agrA |
ARO:3003804 |
not organism-specific |
— |
- ARO:3003804 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| daptomycin resistant cls |
ARO:3003272 |
not organism-specific |
— |
- ARO:3003272 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| daptomycin resistant drmA |
ARO:3003814 |
not organism-specific |
— |
- ARO:3003814 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| daptomycin resistant gdpD |
ARO:3003802 |
not organism-specific |
— |
- ARO:3003802 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| daptomycin resistant mprF |
ARO:3003091 |
not organism-specific |
— |
- ARO:3003091 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| daptomycin resistant pgsA |
ARO:3003080 |
not organism-specific |
— |
- ARO:3003080 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| daptomycin resistant walK |
ARO:3003795 |
not organism-specific |
— |
- ARO:3003795 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| daptomycin-resistant beta prime subunit of RNA polymerase (rpoC) |
ARO:3003290 |
not organism-specific |
— |
- ARO:3003290 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
| daptomycin-resistant beta-subunit of RNA polymerase (rpoB) |
ARO:3003090 |
not organism-specific |
— |
- ARO:3003090 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
ANTIBIOTIC_EFFLUX 1
ANTIBIOTIC_EFFLUX
| Determinant | ARO ID | Organism | Gene families | Evidence |
|---|
| abcA |
ARO:3003942 |
not organism-specific |
— |
- ARO:3003942 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000068 (daptomycin); database assertion, not a primary citation.)
|
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.
Nodes — daptomycin_phosphatidylglycerol_membrane_depolarization
| Node | Label | Type | Grounding |
|---|
daptomycin |
daptomycin |
COMPOUND |
CHEBI:600103 |
calcium_ion |
calcium(2+) |
CHEMICAL |
CHEBI:29108 |
phosphatidylglycerol_rich_membrane |
phosphatidylglycerol-rich bacterial membrane |
CELL_STRUCTURE |
REVIEWED_LABEL_ONLY |
daptomycin_pg_complex |
calcium-dependent daptomycin-phosphatidylglycerol complex |
STATE |
REVIEWED_LABEL_ONLY |
membrane_insertion |
selective daptomycin uptake into the bacterial membrane |
TRANSPORT_PROCESS |
REVIEWED_LABEL_ONLY |
membrane_potential |
bacterial membrane potential |
QUALITY |
REVIEWED_LABEL_ONLY |
Edges — daptomycin_phosphatidylglycerol_membrane_depolarization
| Subject | Predicate | Object | Evidence |
|---|
daptomycin |
participates in |
daptomycin_pg_complex |
- PMID:40455071 (Machhua and colleagues found stable daptomycin-phosphatidylglycerol complex formation in vitro and in drug-treated bacterial membranes.)
|
calcium_ion |
is required for |
daptomycin_pg_complex |
- PMID:40455071 (The phosphatidylglycerol uptake study characterized daptomycin membrane insertion as calcium-dependent.)
|
phosphatidylglycerol_rich_membrane |
participates in |
daptomycin_pg_complex |
- PMID:40455071 (Phosphatidylglycerol was shown to recruit daptomycin to the bacterial membrane and enable selective uptake.)
|
daptomycin_pg_complex |
promotes |
membrane_insertion |
- PMID:40455071 (The study connected stable complex formation with selective daptomycin insertion into model and bacterial membranes.)
|
membrane_insertion |
dissipates |
membrane_potential |
- PMID:1666494 (Daptomycin caused calcium-dependent dissipation of membrane potential in growing Staphylococcus aureus.)
|
Curation history
-
SEEDED_FROM_SOURCES
2026-08-30 · seed_from_sources
Seeded from data/raw/ inventories (ARO, CHEBI)
-
RESEEDED_FROM_SOURCES
2026-08-30 · seed_from_sources
Re-seeded from updated data/raw/ inventories
-
RESEEDED_FROM_SOURCES
2026-08-30 · seed_from_sources
Re-seeded from updated data/raw/ inventories
-
RESEEDED_FROM_SOURCES
2026-08-31 · seed_from_sources
Re-seeded from updated data/raw/ inventories
-
CURATED_CAUSAL_GRAPH
2026-09-04 · codex · LLM-assisted
Added a PMID-supported causal graph for calcium-dependent daptomycin-phosphatidylglycerol membrane targeting.
Provenance
Seeded by scripts/seed_from_sources.py from the committed
inventories in data/raw/.
View the record.