coformycin
CHEBI:16213 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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.
An N-glycosyl in which (8R)-3,6,7,8-tetrahydroimidazo[4,5-d][1,3]diazepin-8-ol is attached to ribofuranose via a β-N3-glycosidic bond. compound The parent of the class of coformycins.
Structure
| Standard InChIKey | YOOVTUPUBVHMPG-LODYRLCVSA-N |
|---|---|
| SMILES | OC[C@H]1O[C@@H](N2C=NC3=C2NC=NC[C@H]3O)[C@H](O)[C@@H]1O |
| Stereochemistry | fully defined |
| Cross-references | npatlas:NPA032755, pubchem:25447 |
Filing pathway
Carbohydrates — 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 other, saccharide, from MIBiG.
Producer organisms 4
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 |
|---|---|---|---|
| Micromonospora haikouensis NCBITaxon:686309 |
BGC_CHARACTERIZED | mibig:BGC0002435 | PMID:30217843 |
| Nocardia interforma ATCC 21072 NCBITaxon:1311815 |
SOURCE_ASSERTION | mibig:BGC0002039 | DOI:10.1128/aac.42.6.1424 |
| Streptomyces kaniharaensis NCBITaxon:212423 |
SOURCE_ASSERTION | mibig:BGC0002040 | DOI:10.1128/aac.42.6.1424 |
| Streptomyces kaniharaensis NCBITaxon:212423 |
SOURCE_ASSERTION | mibig:BGC0002462 | PMID:32350138 |
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.
| Taxon | Source | Reference |
|---|---|---|
| Streptomyces NCBITaxon:1883 |
LOTUS | DOI:10.7164/ANTIBIOTICS.39.309 |
| Streptomyces antibioticus NCBITaxon:1890 |
LOTUS | DOI:10.1021/BI00415A059 |
| Streptomyces antibioticus NCBITaxon:1890 |
LOTUS | DOI:10.7164/ANTIBIOTICS.45.1914 |
Biosynthetic gene clusters 4
| Accession | Host | Locus evidence | Genome |
|---|---|---|---|
| mibig:BGC0002435 | Micromonospora haikouensis NCBITaxon:686309 |
CLUSTER_DEMONSTRATED | genbank:FMCW01000024.1 |
| mibig:BGC0002039 | Nocardia interforma ATCC 21072 NCBITaxon:1311815 |
CLUSTER_UNSTATED | genbank:KY682079.1 |
| mibig:BGC0002040 | Streptomyces kaniharaensis NCBITaxon:212423 |
CLUSTER_UNSTATED | genbank:KY705052.1 |
| mibig:BGC0002462 | Streptomyces kaniharaensis NCBITaxon:212423 |
CLUSTER_DEMONSTRATED | genbank:MK830994.1 |
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.
Biosynthesis curated
Written by a curator with claim-level evidence on each step; not derived from a source. This is what the rest of the record exists to support.
| Step | Enzyme | Reaction | Substrate → product | Evidence |
|---|---|---|---|---|
| 1 | CofB UniProtKB:A0A8A6W587 |
ungrounded → ungrounded | DOI:10.1073/pnas.2000111117 |
Step 1: This curates the Streptomyces kaniharaensis SF-557 CofB SAICAR-synthetase homolog from the BGC0002462/MK830994.1 route; CofB converts a shared L-histidine-pathway branch point intermediate to 8-ketocoformycin-5'-monophosphate. The substrate and product remain ungrounded because exact ChEBI terms were not found for the pathway-specific intermediates.
Mechanism & Biosynthesis Overview
Causal graph — biosynthesis 3 nodes, 2 edges
Partial Streptomyces kaniharaensis coformycin biosynthesis graph for the CofB branch from L-histidine biosynthesis to 8-ketocoformycin-5'-monophosphate.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| shared L-histidine/coformycin branch point intermediate | is converted by | CofB | The substrate is the shared branch-point intermediate between L-histidine and coformycin biosynthesis. | DOI:10.1073/pnas.2000111117 |
| CofB | forms | 8-ketocoformycin-5'-monophosphate | The product is the branch-committed 8-ketocoformycin-5'-monophosphate intermediate rather than mature coformycin. | DOI:10.1073/pnas.2000111117 |
Every edge carries its own citation; an uncited edge is refused by the corpus tests.
Elsewhere in the fleet
- AntibioticMech — CHEBI:16213 (same structure, same inchikey)
Explore across X-Mech
Open questions 1
shared-structure — This structure is reported by more than one MIBiG entry: BGC0002039, BGC0002040, BGC0002435, BGC0002462. Confirm they describe the same compound rather than an upstream cross-reference error.
Provenance
| Source concept | Source | Version |
|---|---|---|
| BGC0002435 | MIBIG | 3 |
| BGC0002039 | MIBIG | 3 |
| BGC0002040 | MIBIG | 3 |
| BGC0002462 | MIBIG | 3 |
| CHEBI:16213 | CHEBI | 3-star |
This page is generated from data/natural_products/carbohydrates/coformycin.yaml, which is generated from the committed inventories. Neither is edited by hand.