urdamycin

naturalproductmech:mibig-d03621b0c2 MINTED SEEDED

Grounding review: No 3-star ChEBI entry shares this structure, so the record keeps a content-hashed identifier.

What these status tags mean

Curation status describes a workflow state. SEEDED means the record entered through the source-seeding workflow; it does not imply that no later curation occurred. PROPOSED marks an addition awaiting review; REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record. These are workflow decisions, not independently verified human review. Agent-assisted contributions may appear in the record history.

Grounding describes the identifier mapping: EXACT uses an ontology identity asserted by the source; MINTED keeps a local identifier when no defensible ontology identity is available; REVIEW_NEEDED flags an exact structure whose ontology identity needs adjudication. The grounding note retains any unresolved alternatives. These tags do not establish the strength of producer or activity evidence.

Structure

Standard InChIKey	WDNBUGBJVRAIKE-JGRVRNPESA-N
SMILES	C[C@H]1[C@H](CC[C@@H](O1)O[C@]23C(=O)C[C@](C[C@]2(C(=CC4=C3C(=O)C5=C(C4=O)C(=C(C=C5)[C@H]6C[C@H]([C@@H]([C@H](O6)C)O)O[C@H]7CC[C@@H]([C@@H](O7)C)O[C@H]8C[C@H]([C@@H]([C@H](O8)C)O)O)O)SC)O)(C)O)O
Stereochemistry	fully defined
Cross-references	pubchem:175975

Filing pathway

Polyketides — computed by NPClassifier npclassifier.gnps2.org@2026-09-07, which is why it is pinned rather than recomputed. The gene cluster's asserted class is pks, from MIBiG.

Producer organisms 2

A claim that this taxon makes the compound. The basis says what the evidence addressed — a knockout and a database assertion are not the same claim.

Taxon	Basis	Cluster	Evidence
Streptomyces fradiae NCBITaxon:1906	SOURCE_ASSERTION	mibig:BGC0000277	PMID:10658661
Streptomyces fradiae NCBITaxon:1906	SOURCE_ASSERTION	mibig:BGC0000278	PMID:11094336

Occurrences 4

Somebody found the compound in this organism and cited it. That is not a claim that the organism makes it, and nothing here promotes one to the other.

Taxon	Source	Reference
Streptomyces fradiae NCBITaxon:1906	LOTUS	DOI:10.1039/C39890000492
Streptomyces fradiae NCBITaxon:1906	LOTUS	DOI:10.1099/00221287-146-1-147
Streptomyces fradiae NCBITaxon:1906	LOTUS	DOI:10.7164/ANTIBIOTICS.39.1657
Streptomyces fradiae NCBITaxon:1906	LOTUS	DOI:10.7164/ANTIBIOTICS.40.459

Biosynthetic gene clusters 2

Accession	Host	Locus evidence	Genome
mibig:BGC0000277	Streptomyces fradiae NCBITaxon:1906	CLUSTER_UNSTATED	genbank:AF164961.1
mibig:BGC0000278	Streptomyces fradiae NCBITaxon:1906	CLUSTER_UNSTATED	genbank:AF269227.1

A locus claim and a taxon claim are different questions. Heterologous expression settles the first and leaves the second where the isolation report left it.

Mechanism & Biosynthesis Overview

Explore across X-Mech

AntibioticMech (urdamycin) ↗ MediaIngredientMech (naturalproductmech:mibig-d03621b0c2) ↗ TaxonMech: Streptomyces fradiae (NCBITaxon:1906) ↗ TaxonMech: Streptomyces fradiae (NCBITaxon:1906) ↗ PathwayMech (mibig:BGC0000277) ↗ PathwayMech (mibig:BGC0000278) ↗

Open questions 1

shared-structure — This structure is reported by more than one MIBiG entry: BGC0000277, BGC0000278. Confirm they describe the same compound rather than an upstream cross-reference error.

Provenance

Source concept	Source	Version
BGC0000277	MIBIG	5
BGC0000278	MIBIG	3

This page is generated from data/natural_products/polyketides/urdamycin.yaml, which is generated from the committed inventories. Neither is edited by hand.