formycin A

CHEBI:42452 EXACT SEEDED antimicrobial unspecifiedenzyme inhibitor

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	KBHMEHLJSZMEMI-KSYZLYKTSA-N
SMILES	C1=NC2=C(NN=C2C(=N1)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O
Stereochemistry	fully defined
Cross-references	pubchem:447199

Filing pathway

Alkaloids — 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, from MIBiG.

Producer organisms 3

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 kaniharaensis NCBITaxon:212423	BGC_CHARACTERIZED	mibig:BGC0002282	DOI:10.1016/j.bmc.2022.116613
Nocardia interforma ATCC 21072 NCBITaxon:1311815	SOURCE_ASSERTION	mibig:BGC0002039	DOI:10.1016/j.bmc.2022.116613
Streptomyces kaniharaensis NCBITaxon:212423	SOURCE_ASSERTION	mibig:BGC0002040	DOI:10.1016/j.bmc.2022.116613

Occurrences 1

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 sparsogenes NCBITaxon:67365	LOTUS	DOI:10.1016/S0021-9673(01)83861-9

Biosynthetic gene clusters 3

Accession	Host	Locus evidence	Genome
mibig:BGC0002282	Streptomyces kaniharaensis NCBITaxon:212423	CLUSTER_DEMONSTRATED	genbank:WBOF01000001.1
mibig:BGC0002039	Nocardia interforma ATCC 21072 NCBITaxon:1311815	CLUSTER_UNSTATED	genbank:KY682079.1
mibig:BGC0002040	Streptomyces kaniharaensis NCBITaxon:212423	CLUSTER_UNSTATED	genbank:KY705052.1

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

Causal graph — bioactivity 3 nodes, 2 edges

Formycin A binds 5'-methylthioadenosine nucleosidases in E. coli and Arabidopsis thaliana co-crystal structures.

Subject	Predicate	Object	Notes	Evidence
formycin A	binds	Escherichia coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase	PDB 1NC3 maps chains A and B to the historical UniProtKB:P24247 entry for residues 1-232; P24247 is now a secondary accession on active UniProtKB:P0AF12. The PDB FMC ligand resolves to the same Standard InChIKey, ChEBI identifier, and PubChem CID as this record. PubChem BioAssay AID 977610 reports 10 uM Ki rows for 1NC3 chains A and B.	DOI:10.1074/jbc.M210836200 DOI:10.2210/pdb1nc3/pdb reference DOI:10.1074/jbc.M210836200 evidence type PRIMARY_EXPERIMENT snippet Structure of Escherichia coli 5'-methylthioadenosine/ S-adenosylhomocysteine nucleosidase inhibitor complexes notes RCSB PDB lists this article as the primary citation for the 1NC3 formycin A-bound structure. reference DOI:10.2210/pdb1nc3/pdb evidence type DATABASE_ASSERTION snippet E. coli MTA/AdoHcy nucleosidase complexed with formycin A notes RCSB PDB 1NC3 maps the homomeric protein chains to UniProtKB:P24247 and maps FMC to the same Standard InChIKey as CHEBI:42452.
formycin A	binds	Arabidopsis thaliana 5'-methylthioadenosine nucleosidase	PDB 2QTT maps chains A and B to UniProtKB:Q9T0I8 residues 1-267; the structure contains one FMC ligand in author chain B. The PDB FMC ligand resolves to the same Standard InChIKey, ChEBI identifier, and PubChem CID as this record. PubChem BioAssay AID 977610 reports 48 uM Ki rows for 2QTT chains A and B.	DOI:10.1016/j.jmb.2008.01.088 DOI:10.2210/pdb2qtt/pdb reference DOI:10.1016/j.jmb.2008.01.088 evidence type PRIMARY_EXPERIMENT snippet Molecular determinants of substrate specificity in plant 5'-methylthioadenosine nucleosidases notes RCSB PDB lists this article as the primary citation for the 2QTT Arabidopsis MTN1 structure with formycin A. reference DOI:10.2210/pdb2qtt/pdb evidence type DATABASE_ASSERTION snippet Arabidopsis thaliana 5'-Methylthioadenosine nucleosidase in complex with Formycin A notes RCSB PDB 2QTT maps the homomeric protein chains to UniProtKB:Q9T0I8 and maps FMC to the same Standard InChIKey as CHEBI:42452.

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

Bioactivities 5

Entries preserve source qualifiers, targets and evidence. Repeated assay names or values are not independent replications; inspect source detail for differences.

Assay	Result	Target enzyme	Source detail
Experimentally measured binding affinity data (Ki) for protein-ligand complexes derived from PDB	KI 10 uM; ACTIVE	Not recorded	PMID:12496243 assay Experimentally measured binding affinity data (Ki) for protein-ligand complexes derived from PDB evidence reference PMID:12496243 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 977610, deposited by Shanghai Institute of Organic Chemistry; assay type Other. Target accession 1NC3_A was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type KI value 10.0 units uM activity class ENZYME_INHIBITOR
Experimentally measured binding affinity data (Ki) for protein-ligand complexes derived from PDB	KI 10 uM; ACTIVE	Not recorded	PMID:12496243 assay Experimentally measured binding affinity data (Ki) for protein-ligand complexes derived from PDB evidence reference PMID:12496243 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 977610, deposited by Shanghai Institute of Organic Chemistry; assay type Other. Target accession 1NC3_B was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type KI value 10.0 units uM activity class ENZYME_INHIBITOR
Experimentally measured binding affinity data (Ki) for protein-ligand complexes derived from PDB	KI 48 uM; ACTIVE	Not recorded	PMID:18342331 assay Experimentally measured binding affinity data (Ki) for protein-ligand complexes derived from PDB evidence reference PMID:18342331 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 977610, deposited by Shanghai Institute of Organic Chemistry; assay type Other. Target accession 2QTT_A was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type KI value 48.0 units uM activity class ENZYME_INHIBITOR
Experimentally measured binding affinity data (Ki) for protein-ligand complexes derived from PDB	KI 48 uM; ACTIVE	Not recorded	PMID:18342331 assay Experimentally measured binding affinity data (Ki) for protein-ligand complexes derived from PDB evidence reference PMID:18342331 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 977610, deposited by Shanghai Institute of Organic Chemistry; assay type Other. Target accession 2QTT_B was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type KI value 48.0 units uM activity class ENZYME_INHIBITOR
Experimentally measured binding affinity data derived from PDB	ACTIVE	Not recorded	PMID:12496243 assay Experimentally measured binding affinity data derived from PDB evidence reference PMID:12496243 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1811, deposited by Shanghai Institute of Organic Chemistry; assay type Other. Target accession 1NC3_A was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE activity class ENZYME_INHIBITOR

Elsewhere in the fleet

AntibioticMech — CHEBI:42452 (same structure, same inchikey)

Explore across X-Mech

AntibioticMech (formycin A) ↗ MediaIngredientMech (CHEBI:42452) ↗ TaxonMech: Streptomyces kaniharaensis (NCBITaxon:212423) ↗ TaxonMech: Nocardia interforma ATCC 21072 (NCBITaxon:1311815) ↗ TaxonMech: Streptomyces kaniharaensis (NCBITaxon:212423) ↗ PathwayMech (mibig:BGC0002282) ↗ PathwayMech (mibig:BGC0002039) ↗ PathwayMech (mibig:BGC0002040) ↗

Open questions 1

shared-structure — This structure is reported by more than one MIBiG entry: BGC0002039, BGC0002040, BGC0002282. Confirm they describe the same compound rather than an upstream cross-reference error.

Provenance

Source concept	Source	Version
BGC0002282	MIBIG	2
BGC0002039	MIBIG	3
BGC0002040	MIBIG	3
CHEBI:42452	CHEBI	3-star

This page is generated from data/natural_products/alkaloids/formycin-a.yaml, which is generated from the committed inventories. Neither is edited by hand.