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geldanamycin

CHEBI:5292 EXACT SEEDED antiviral

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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.

An ansamycin consisting of a 19-membered macrocyle incorporating a benzoquinone ring and a lactam functionality. It shows antimicrobial activity against many Gram-positive and some Gram-negative bacteria.

Structure

Standard InChIKeyQTQAWLPCGQOSGP-KSRBKZBZSA-N
SMILESC[C@H]1C[C@@H]([C@@H]([C@H](/C=C(/[C@@H]([C@H](/C=C\C=C(\C(=O)NC2=CC(=O)C(=C(C1)C2=O)OC)/C)OC)OC(=O)N)\C)C)O)OC
Stereochemistryfully defined
Cross-referencespubchem:5288382

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.

TaxonBasisClusterEvidence
Streptomyces hygroscopicus subsp. duamyceticus
NCBITaxon:285527		 SOURCE_ASSERTION mibig:BGC0000067 PMID:18600054
Streptomyces hygroscopicus
NCBITaxon:1912		 SOURCE_ASSERTION mibig:BGC0000068 PMID:18214443

Occurrences 3

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.

TaxonSourceReference
Streptomyces hygroscopicus
NCBITaxon:1912		 LOTUS DOI:10.1007/S00203-007-0346-2
Streptomyces hygroscopicus
NCBITaxon:1912		 LOTUS DOI:10.1021/NP4000679
Streptomyces hygroscopicus
NCBITaxon:1912		 LOTUS DOI:10.1021/NP50047A016

Biosynthetic gene clusters 2

AccessionHostLocus evidenceGenome
mibig:BGC0000067 Streptomyces hygroscopicus subsp. duamyceticus
NCBITaxon:285527 		CLUSTER_UNSTATED genbank:DQ249341.1
mibig:BGC0000068 Streptomyces hygroscopicus
NCBITaxon:1912 		CLUSTER_UNSTATED genbank:DQ914285.1

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

PRODUCERS & OCCURRENCE 2 producers (0 causal) 3 cited occurrences BIOSYNTHETIC LOCUS 2 gene clusters 0 curated pathway steps NATURAL PRODUCT geldanamycin CHEBI:5292 Polyketides TARGETS & BIOACTIVITY 0 molecular targets 0 bioactivities · 1 graph

Causal graph — bioactivity 2 nodes, 1 edge

Geldanamycin binds the N-terminal ATPase domain of human HSP90-alpha.

SubjectPredicateObjectNotesEvidence
geldanamycin binds human heat shock protein HSP 90-alpha RCSB PDB 1YET contains the GDM ligand with the exact QTQAWLPCGQOSGP-KSRBKZBZSA-N structure. RCSB/SIFTS maps the 228-residue deposited chain A sequence to UniProtKB:P07900 positions 9-236 (accessed 2026-10-14). Comparison with the current UniProt sequence shows deposited T versus reference S at position 63; the cause is not adjudicated and this is not an assertion of an engineered mutation. The paper abstract describes the structural domain as residues 9-232, distinct from the deposited construct-to-reference mapping.
DOI:10.1016/S0092-8674(00)80203-2
https://data.rcsb.org/rest/v1/core/polymer_entity/1YET/1
  • reference
    DOI:10.1016/S0092-8674(00)80203-2
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    Crystal structure of an Hsp90-geldanamycin complex: targeting of a protein chaperone by an antitumor agent.
    notes
    Stebbins et al. solved PDB 1YET with geldanamycin in the human HSP90 N-terminal geldanamycin-binding domain.
  • reference
    https://data.rcsb.org/rest/v1/core/polymer_entity/1YET/1
    evidence type
    DATABASE_ASSERTION
    notes
    SIFTS maps entity1 residues1-228 to P07900 starting at9. Current sequence comparison and registry receipts are retained in reviews/evidence/20261014-geldanamycin/; this mapping evidence is separate from the primary binding experiment.

Every edge carries its own citation; an uncited edge is refused by the corpus tests.

Elsewhere in the fleet

Explore across X-Mech

AntibioticMech (geldanamycin) ↗ MediaIngredientMech (CHEBI:5292) ↗ TaxonMech: Streptomyces hygroscopicus subsp. duamyceticus (NCBITaxon:285527) ↗ TaxonMech: Streptomyces hygroscopicus (NCBITaxon:1912) ↗ PathwayMech (mibig:BGC0000067) ↗ PathwayMech (mibig:BGC0000068) ↗

Open questions 1

shared-structure — This structure is reported by more than one MIBiG entry: BGC0000067, BGC0000068. Confirm they describe the same compound rather than an upstream cross-reference error.

Provenance

Source conceptSourceVersion
BGC0000067MIBIG5
BGC0000068MIBIG5
CHEBI:5292CHEBI3-star

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