kanamycin A

CHEBI:17630 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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.

Structure

Standard InChIKey	SBUJHOSQTJFQJX-NOAMYHISSA-N
SMILES	C1[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)O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)N)O)N
Stereochemistry	fully defined
Cross-references	pubchem:6032

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 5

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 kanamyceticus NCBITaxon:1967	SOURCE_ASSERTION	mibig:BGC0000702	PMID:15303497
Streptomyces kanamyceticus NCBITaxon:1967	SOURCE_ASSERTION	mibig:BGC0000703	PMID:16766657
Streptomyces kanamyceticus NCBITaxon:1967	SOURCE_ASSERTION	mibig:BGC0000704	PMID:15313224
Streptomyces kanamyceticus NCBITaxon:1967	SOURCE_ASSERTION	mibig:BGC0000705	PMID:19362651
Streptomyces kanamyceticus NCBITaxon:1967	SOURCE_ASSERTION	mibig:BGC0000706	PMID:16766657

Occurrences 24

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
Hohenbuehelia grisea NCBITaxon:104357	LOTUS	DOI:10.1021/ACS.JNATPROD.7B00713
Nocardia abscessus NCBITaxon:120957	LOTUS	DOI:10.1021/ACS.JNATPROD.6B00935
Sparticola junci NCBITaxon:1803578	LOTUS	DOI:10.1021/ACS.JNATPROD.9B00604
Verrucosispora NCBITaxon:1873	LOTUS	DOI:10.1021/ACS.JNATPROD.9B00654
Streptomyces NCBITaxon:1883	LOTUS	DOI:10.1021/ACS.JNATPROD.0C00161
Streptomyces NCBITaxon:1883	LOTUS	DOI:10.1021/JA01548A077
Streptomyces hygroscopicus NCBITaxon:1912	LOTUS	DOI:10.1021/NP400145U
Aspergillus porosus NCBITaxon:1924929	LOTUS	DOI:10.1021/ACS.JNATPROD.9B00416
Streptomyces niveus NCBITaxon:193462	LOTUS	DOI:10.1021/NP4006025
Elateriospermum tapos NCBITaxon:212299	LOTUS	DOI:10.1021/NP070629G
Actinoalloteichus cyanogriseus NCBITaxon:2893586	LOTUS	DOI:10.1021/NP4006025
Phoma NCBITaxon:37463	LOTUS	DOI:10.1021/ACS.JNATPROD.8B00685
Armillaria NCBITaxon:47424	LOTUS	DOI:10.1021/ACS.JNATPROD.8B00685
Pseudoalteromonas NCBITaxon:53246	LOTUS	DOI:10.1021/NP500775E
Streptomyces venezuelae NCBITaxon:54571	LOTUS	DOI:10.1007/S00253-007-1096-4
Myrothecium NCBITaxon:5531	LOTUS	DOI:10.1021/NP500142G
Streptomyces canus NCBITaxon:58343	LOTUS	DOI:10.1021/JF305210U
Micromonospora harpali NCBITaxon:686309	LOTUS	DOI:10.1021/ACS.JNATPROD.7B00176
Serratia plymuthica NCBITaxon:82996	LOTUS	DOI:10.1021/ACS.JNATPROD.7B00565
Streptomyces kanamyceticus NCBITaxon:1967	LOTUS	DOI:10.1016/J.ABB.2004.06.009
Streptomyces kanamyceticus NCBITaxon:1967	LOTUS	DOI:10.1073/PNAS.0603251103
Streptomyces kanamyceticus NCBITaxon:1967	LOTUS	DOI:10.1271/BBB1961.39.1593
Streptomyces kanamyceticus NCBITaxon:1967	LOTUS	DOI:10.1371/JOURNAL.PONE.0181971
Streptomyces kanamyceticus NCBITaxon:1967	LOTUS	DOI:10.7164/ANTIBIOTICS.57.351

Biosynthetic gene clusters 5

Accession	Host	Locus evidence	Genome
mibig:BGC0000702	Streptomyces kanamyceticus NCBITaxon:1967	CLUSTER_UNSTATED	genbank:AB164642.1
mibig:BGC0000703	Streptomyces kanamyceticus NCBITaxon:1967	CLUSTER_UNSTATED	genbank:CP023699.1
mibig:BGC0000704	Streptomyces kanamyceticus NCBITaxon:1967	CLUSTER_UNSTATED	genbank:AJ582817.3
mibig:BGC0000705	Streptomyces kanamyceticus NCBITaxon:1967	CLUSTER_UNSTATED	genbank:AJ628422.2
mibig:BGC0000706	Streptomyces kanamyceticus NCBITaxon:1967	CLUSTER_UNSTATED	genbank:AB254081.1

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

Bioactivities 2

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
Primary qHTS for inhibitors of SARS-S pseudo-typed particle cell entry	OTHER 3.9811 uM; NOT_DETERMINED	UniProtKB:P59594	pubchem.aid:1479145 assay Primary qHTS for inhibitors of SARS-S pseudo-typed particle cell entry evidence reference pubchem.aid:1479145 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1479145, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. call NOT_DETERMINED measurement type OTHER value 3.9811 units uM target enzyme UniProtKB:P59594
DSSTox (FDAMDD) FDA Maximum (Recommended) Daily Dose Database	ACTIVE	Not 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

Elsewhere in the fleet

AntibioticMech — CHEBI:17630 (same structure, same inchikey)

Explore across X-Mech

AntibioticMech (kanamycin A) ↗ MediaIngredientMech (CHEBI:17630) ↗ TaxonMech: Streptomyces kanamyceticus (NCBITaxon:1967) ↗ TaxonMech: Streptomyces kanamyceticus (NCBITaxon:1967) ↗ TaxonMech: Streptomyces kanamyceticus (NCBITaxon:1967) ↗ TaxonMech: Streptomyces kanamyceticus (NCBITaxon:1967) ↗ PathwayMech (mibig:BGC0000702) ↗ PathwayMech (mibig:BGC0000703) ↗ PathwayMech (mibig:BGC0000704) ↗

Open questions 1

shared-structure — This structure is reported by more than one MIBiG entry: BGC0000702, BGC0000703, BGC0000704, BGC0000705, BGC0000706. Confirm they describe the same compound rather than an upstream cross-reference error.

Provenance

Source concept	Source	Version
BGC0000702	MIBIG	5
BGC0000703	MIBIG	4
BGC0000704	MIBIG	3
BGC0000705	MIBIG	3
BGC0000706	MIBIG	3
CHEBI:17630	CHEBI	3-star

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