romidepsin
CHEBI:61080 EXACT SEEDED antimicrobial unspecified
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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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.
A cyclodepsipeptide consisting of the cyclic disulfide of (2Z)-2-aminobut-2-enoyl, L-valyl, (3S,4E)-3-hydroxy-7-sulfanylhept-4-enoyl, D-valyl and D-cysteinyl residues coupled in sequence and cyclised head-to tail.
Structure
| Standard InChIKey | OHRURASPPZQGQM-GCCNXGTGSA-N |
|---|---|
| SMILES | C\C=C1/NC(=O)[C@H]2CSSCC\C=C\[C@H](CC(=O)N[C@H](C(C)C)C(=O)N2)OC(=O)[C@@H](NC1=O)C(C)C |
| Stereochemistry | fully defined |
| Cross-references | npatlas:NPA016792 |
Filing pathway
Unclassified — 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 nrps, pks, from MIBiG.
Producer organisms 1
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 |
|---|---|---|---|
| Chromobacterium violaceum NCBITaxon:536 |
BGC_CHARACTERIZED | mibig:BGC0000993 | PMID:17400765 |
Occurrences 5
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 |
|---|---|---|
| Humicola fuscoatra NCBITaxon:112175 |
LOTUS | DOI:10.1021/NP400889X |
| Chromobacterium violaceum NCBITaxon:536 |
LOTUS | DOI:10.1128/AEM.01751-06 |
| Chromobacterium violaceum NCBITaxon:536 |
LOTUS | DOI:10.7164/ANTIBIOTICS.47.301 |
| Chromobacterium violaceum NCBITaxon:536 |
CHEBI | PMID:21793558 |
| Chromobacterium violaceum NCBITaxon:536 |
CHEBI | PMID:21967146 |
Biosynthetic gene clusters 1
| Accession | Host | Locus evidence | Genome |
|---|---|---|---|
| mibig:BGC0000993 | Chromobacterium violaceum NCBITaxon:536 |
CLUSTER_DEMONSTRATED | genbank:EF210776.1 |
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
Elsewhere in the fleet
- AntibioticMech — CHEBI:61080 (same structure, same inchikey)
Explore across X-Mech
Open questions 1
name-disagreement — ChEBI calls this structure 'romidepsin' and MIBiG calls it 'FR901228'. They share a Standard InChIKey, so if the names denote different compounds then one upstream record has the wrong structure. Check which.
Provenance
| Source concept | Source | Version |
|---|---|---|
| BGC0000993 | MIBIG | 4 |
| CHEBI:61080 | CHEBI | 3-star |
This page is generated from data/natural_products/unclassified/romidepsin.yaml, which is generated from the committed inventories. Neither is edited by hand.