coumermycin A1

CHEBI:3907 ·resolve ·ANTIBACTERIAL ·EXACT SEEDED

A hydroxycoumarin antibiotic that is obtained from Streptomyces rishiriensis and exhibits potent antibacterial and anticancer activity. — 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

aminocoumarin antibioticARO:3000103

Strictly broader compounds or drug classes this molecule belongs to.

Label unavailable CHEBI:23403
Label unavailable CHEBI:24400
Label unavailable CHEBI:26455
Label unavailable CHEBI:38064
Label unavailable CHEBI:62733
aminocoumarin antibiotic ARO:3000103

Chemical structure

Computed structure properties
Molecular formula	C55H59N5O20
Charge	0
Average mass	1110.092 Da
Monoisotopic mass	1109.37534 Da
Source	ChEBI
InChIKey	WTIJXIZOODAMJT-DHFGXMAYSA-N

SMILES

CO[C@@H]1[C@@H](OC(=O)c2ccc(C)n2)[C@@H](O)[C@H](Oc2ccc3c(O)c(NC(=O)c4cnc(C(=O)Nc5c(O)c6ccc(O[C@@H]7OC(C)(C)[C@H](OC)[C@@H](OC(=O)c8ccc(C)n8)[C@H]7O)c(C)c6oc5=O)c4C)c(=O)oc3c2C)OC1(C)C

InChI

InChI=1S/C55H59N5O20/c1-21-12-16-29(57-21)48(67)77-42-38(63)52(79-54(6,7)44(42)71-10)73-31-18-14-26-36(61)34(50(69)75-40(26)24(31)4)59-46(65)28-20-56-33(23(28)3)47(66)60-35-37(62)27-15-19-32(25(5)41(27)76-51(35)70)74-53-39(64)43(45(72-11)55(8,9)80-53)78-49(68)30-17-13-22(2)58-30/h12-20,38-39,42-45,52-53,56-58,61-64H,1-11H3,(H,59,65)(H,60,66)/t38-,39-,42+,43+,44-,45-,52-,53-/m1/s1

Also called

coumamycine (INN)— chebi
coumamycinum (INN)— chebi
cumamicina (INN)— chebi
(3-methyl-1H-pyrrole-2,4-diyl)bis[carbonylimino(4-hydroxy-8-methyl-2-oxo-2H-chromene-3,7-diyl)oxy(2R,3R,4S,5R)-3-hydroxy-5-methoxy-6,6-dimethyltetrahydro-2H-pyran-2,4-diyl] bis(5-methyl-1H-pyrrole-2-carboxylate) (EXACT_SYNONYM)— chebi
Coumermycin (EXACT_SYNONYM)— chebi
NSC 107412 (EXACT_SYNONYM)— chebi
Notomycin (EXACT_SYNONYM)— chebi
Notomycin A1 (EXACT_SYNONYM)— chebi
Sugordomycin D-1a (EXACT_SYNONYM)— chebi

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.

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.

kegg.drug:D02333

Patents and articles

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

wikipedia.en:Coumermycin_A1

Activity roles

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

antimicrobial agent CHEBI:33281

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:3000150`	coumermycin A1	`antibioticmech:aro-cc3947c3d9`	2026-08-30
CHEBI	`CHEBI:3907`	coumermycin A1	`antibioticmech:chebi-977895c932`	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.

aminocoumarin sensitive parE PROTEIN DIRECT_BINDING_TARGET

ARO:3000023

CARD/ARO database assertion; target organism, strain, and assay are not specified. Topoisomerase IV subunit asserted as the aminocoumarin-sensitive target. Evidence status: PRIMARY_EVIDENCE_NEEDED. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

ARO:3000023 (CARD/ARO asserts targeted_by_antibiotic ARO:3000150 (coumermycin A1); database assertion, not a primary citation.)

antibiotic sensitive DNA topoisomerase subunit gyrB PROTEIN DIRECT_BINDING_TARGET

ARO:3000734

CARD/ARO database assertion; target organism, strain, and assay are not specified. ARO explicitly describes ligand binding to gyrase subunit B. Evidence status: PRIMARY_EVIDENCE_NEEDED. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

ARO:3000734 (CARD/ARO asserts targeted_by_antibiotic ARO:3000150 (coumermycin A1); database assertion, not a primary citation.)

aminocoumarin sensitive parY PROTEIN DIRECT_BINDING_TARGET

ARO:3003253

CARD/ARO database assertion; target organism, strain, and assay are not specified. ParY is asserted as the aminocoumarin-sensitive subunit. Evidence status: PRIMARY_EVIDENCE_NEEDED. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

ARO:3003253 (CARD/ARO asserts targeted_by_antibiotic ARO:3000150 (coumermycin A1); database assertion, not a primary citation.)

aminocoumarin sensitive gyrB PROTEIN DIRECT_BINDING_TARGET

ARO:3003260

CARD/ARO database assertion; target organism, strain, and assay are not specified. GyrB is asserted as the aminocoumarin-sensitive subunit. Evidence status: PRIMARY_EVIDENCE_NEEDED. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

ARO:3003260 (CARD/ARO asserts targeted_by_antibiotic ARO:3000150 (coumermycin A1); database assertion, not a primary citation.)

Mechanism summary

Mode of action: NUCLEIC_ACID_SYNTHESIS_INHIBITION microbial target — Assigned from ChEBI role CHEBI:53559 (topoisomerase IV inhibitor), CHEBI:59517 (DNA synthesis inhibitor). ChEBI asserts the role on the compound. The role names a target specific to the microbe or virus — see mode_of_action_target_scope. Not a curator's mechanistic review.

Resistance mechanisms

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

ANTIBIOTIC_TARGET_ALTERATION 5

ANTIBIOTIC_TARGET_ALTERATION
Determinant	ARO ID	Organism	Gene families	Evidence
Bartonella bacilliformis gyrB conferring resistance to aminocoumarin	ARO:3003302	not organism-specific	—	ARO:3003302 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000150 (coumermycin A1); database assertion, not a primary citation.)
Escherichia coli gyrB conferring resistance to aminocoumarin	ARO:3003303	not organism-specific	—	ARO:3003303 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000150 (coumermycin A1); database assertion, not a primary citation.)
Staphylococcus aureus gyrB conferring resistance to aminocoumarin	ARO:3003301	not organism-specific	—	ARO:3003301 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000150 (coumermycin A1); database assertion, not a primary citation.)
Staphylococcus aureus parE conferring resistance to aminocoumarin	ARO:3003314	not organism-specific	—	ARO:3003314 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000150 (coumermycin A1); database assertion, not a primary citation.)
Streptomyces rishiriensis parY mutant conferring resistance to aminocoumarin	ARO:3003318	not organism-specific	—	ARO:3003318 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000150 (coumermycin A1); database assertion, not a primary citation.)

UNKNOWN 1

UNKNOWN
Determinant	ARO ID	Organism	Gene families	Evidence
ParYR-associated reduced susceptibility to coumermycin A1 The comparison concerns laboratory derivatives of the TK24 background, not native-donor susceptibility or species-wide resistance. NCBITaxon:457428 denotes the TK24 background, not the experimental derivative. The reported donor is Streptomyces rishiriensis DSM 40489. UniProtKB:Q83WB8 is reference-only (entry version 120, sequence version 2); the archive succession does not establish the exact experimental allele. The 2003 study leaves ParY enzymatic function unresolved. No induced point mutant, clinical category, numerical AST, derivative TaxID or experimental genome is assigned. Compound scope follows the source's named structure in Figure 1A, not independent re-identification of the tested preparation.	—	Streptomyces lividans `NCBITaxon:1916`	parYR	PMID:12604514 (Relevant publisher-indexed Results text was inspected before the later article request returned 403; native Figure 1A was visually inspected separately. Native Table 2 and complete paper review remain open.) Qualitative source-reported laboratory-host growth comparison

Producer organisms

Organisms that biosynthesize this compound. Cluster link evidence is how the upstream source graded the gene cluster, so it is populated only for a source that grades it. An empty cell is not weaker support: a curator-authored producer carries its support in Evidence instead. Where the source entry named several compounds, the evidence is marked inherited, meaning it covers this compound together with the cluster's other products rather than singling it out. Those products need not be related to each other: a cluster can list an intermediate, a precursor and a finished antibiotic side by side.

Producer organisms
Organism	BGC	Cluster link evidence	Source	Quality	Note	Evidence
Streptomyces rishiriensis NCBITaxon:68264	BGC0000833	Enzymatic assays; Heterologous expression; Knock-out studies compound specific	MIBIG 4.0.1 (entry 4)	questionable	MIBiG active entry; compound 'coumermycin A1' joined by exact Standard InChIKey.	PMID:14285468 (MIBiG's first legacy reference for the entry, inherited rather than attached to the compound. It supports that the entry exists; it is NOT established as evidence for this specific producer/compound link.)

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
RESEEDED_FROM_SOURCES 2026-09-08 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-09-08 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-09-10 · seed_from_sources
Re-seeded from updated data/raw/ inventories
CURATED_RESISTANCE_EVIDENCE 2026-10-10 · codex · LLM-assisted
Added one qualitative primary-backed ParYR-associated host susceptibility finding; preserved donor/host/reference distinctions and all existing source slices. No exact allele, numerical AST or genome assigned. Whole-record review remains open.

Provenance

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

Explore across X-Mech: MediaIngredientMech (coumermycin A1) · CultureMech · NaturalProductMech · PathwayMech · TraitMech · TaxonMech (Streptomyces rishiriensis)