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framycetin

CHEBI:7508 EXACT SEEDED antibacterial

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 tetracyclic antibacterial agent derived from neomycin, being a glycoside ester of neamine and neobiosamine B.

Structure

Standard InChIKeyPGBHMTALBVVCIT-VCIWKGPPSA-N
SMILESC1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CN)O)O)N)O[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O[C@@H]4[C@@H]([C@H]([C@@H]([C@@H](O4)CN)O)O)N)O)O)N
Stereochemistryfully defined
Cross-referencespubchem:8378

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 saccharide, 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.

TaxonBasisClusterEvidence
Streptomyces fradiae
NCBITaxon:1906		 SOURCE_ASSERTION mibig:BGC0000711 PMID:15827636

Occurrences 18

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 albus
NCBITaxon:1888		 LOTUS DOI:10.1002/JOBM.3630170504
Streptomyces rimosus
NCBITaxon:1927		 LOTUS DOI:10.1016/0006-291X(84)91367-6
Streptomyces fradiae
NCBITaxon:1906		 LOTUS DOI:10.1007/S00253-018-09597-8
Streptomyces fradiae
NCBITaxon:1906		 LOTUS DOI:10.1007/S10059-009-0008-0
Streptomyces fradiae
NCBITaxon:1906		 LOTUS DOI:10.1007/S11427-017-9120-8
Streptomyces fradiae
NCBITaxon:1906		 LOTUS DOI:10.1007/S12223-011-0082-5
Streptomyces fradiae
NCBITaxon:1906		 LOTUS DOI:10.1016/J.JBIOTEC.2013.03.015
Streptomyces fradiae
NCBITaxon:1906		 LOTUS DOI:10.1016/S0021-9673(00)94512-6
Streptomyces fradiae
NCBITaxon:1906		 LOTUS DOI:10.1039/B501199J
Streptomyces fradiae
NCBITaxon:1906		 LOTUS DOI:10.1039/C39870000012
Streptomyces fradiae
NCBITaxon:1906		 LOTUS DOI:10.1042/BJ1220397
Streptomyces fradiae
NCBITaxon:1906		 LOTUS DOI:10.1099/00221287-121-2-477
Streptomyces fradiae
NCBITaxon:1906		 LOTUS DOI:10.1128/AM.13.2.190-193.1965
Streptomyces fradiae
NCBITaxon:1906		 LOTUS DOI:10.1128/AM.15.4.744-749.1967
Streptomyces fradiae
NCBITaxon:1906		 LOTUS DOI:10.1155/2014/674286
Streptomyces fradiae
NCBITaxon:1906		 LOTUS DOI:10.3390/MD12042079
Streptomyces fradiae
NCBITaxon:1906		 LOTUS DOI:10.7164/ANTIBIOTICS.37.77
Streptomyces fradiae
NCBITaxon:1906		 LOTUS DOI:10.7164/ANTIBIOTICS.45.984

Biosynthetic gene clusters 1

AccessionHostLocus evidenceGenome
mibig:BGC0000711 Streptomyces fradiae
NCBITaxon:1906 		CLUSTER_UNSTATED genbank:AJ843080.1

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 1 producer (0 causal) 18 cited occurrences BIOSYNTHETIC LOCUS 1 gene cluster 0 curated pathway steps NATURAL PRODUCT framycetin CHEBI:7508 Carbohydrates TARGETS & BIOACTIVITY 0 molecular targets 2 bioactivities · 0 graphs

Bioactivities 2

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

AssayResultTarget enzymeSource detail
DSSTox (FDAMDD) FDA Maximum (Recommended) Daily Dose DatabaseACTIVENot recorded
pubchem.aid:1195
assay
DSSTox (FDAMDD) FDA Maximum (Recommended) Daily Dose Database
evidence
  • reference
    pubchem.aid:1195
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1195, deposited by EPA DSSTox; assay type Other.
call
ACTIVE
Rat CaS receptor (Calcium-sensing receptor)ACTIVENot recorded
PMID:7816802
assay
Rat CaS receptor (Calcium-sensing receptor)
evidence
  • reference
    PMID:7816802
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1346722, deposited by IUPHAR-DB; assay type Other. Target accession NP_058692 was left ungrounded because PubChem did not provide a UniProtKB accession.
call
ACTIVE

Elsewhere in the fleet

Explore across X-Mech

AntibioticMech (framycetin) ↗ MediaIngredientMech (CHEBI:7508) ↗ TaxonMech: Streptomyces fradiae (NCBITaxon:1906) ↗ PathwayMech (mibig:BGC0000711) ↗

Open questions 1

name-disagreement — ChEBI calls this structure 'framycetin' and MIBiG calls it 'neomycin'. They share a Standard InChIKey, so if the names denote different compounds then one upstream record has the wrong structure. Check which.

Provenance

Source conceptSourceVersion
BGC0000711MIBIG5
CHEBI:7508CHEBI3-star

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