spectinomycin

CHEBI:9215 EXACT SEEDED antibacterialenzyme 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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.

A pyranobenzodioxin and antibiotic that is active against gram-negative bacteria and used (as its dihydrochloride pentahydrate) to treat gonorrhea. It is produced by the bacterium Streptomyces spectabilis.

Structure

Standard InChIKey	UNFWWIHTNXNPBV-WXKVUWSESA-N
SMILES	C[C@@H]1CC(=O)[C@]2([C@@H](O1)O[C@@H]3[C@H]([C@@H]([C@@H]([C@@H]([C@H]3O2)NC)O)NC)O)O
Stereochemistry	fully defined
Cross-references	pubchem:15541

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.

Taxon	Basis	Cluster	Evidence
Streptomyces netropsis NCBITaxon:55404	SOURCE_ASSERTION	mibig:BGC0000716	PMID:9245803

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
Ramaria cystidiophora NCBITaxon:113088	LOTUS	DOI:10.1021/NP3006277
Streptomyces NCBITaxon:1883	LOTUS	DOI:10.7164/ANTIBIOTICS.37.1519
Streptomyces venezuelae NCBITaxon:54571	LOTUS	DOI:10.1002/JOBM.200410529
Streptomyces venezuelae NCBITaxon:54571	LOTUS	DOI:10.1007/S10295-019-02172-8
Streptomyces venezuelae NCBITaxon:54571	LOTUS	DOI:10.1016/J.JBIOTEC.2014.01.028
Streptomyces venezuelae NCBITaxon:54571	LOTUS	DOI:10.1111/J.1365-2672.2008.03788.X
Streptomyces venezuelae NCBITaxon:54571	LOTUS	DOI:10.1111/J.1574-6968.2000.TB08955.X
Streptomyces venezuelae NCBITaxon:54571	LOTUS	DOI:10.1128/JB.177.3.818-822.1995
Streptomyces venezuelae NCBITaxon:54571	LOTUS	DOI:10.7164/ANTIBIOTICS.47.1425
Streptomyces spectabilis NCBITaxon:68270	LOTUS	DOI:10.1002/JOBM.200410529
Streptomyces spectabilis NCBITaxon:68270	LOTUS	DOI:10.1007/S10295-019-02172-8
Streptomyces spectabilis NCBITaxon:68270	LOTUS	DOI:10.1016/J.JBIOTEC.2014.01.028
Streptomyces spectabilis NCBITaxon:68270	LOTUS	DOI:10.1021/JA00875A053
Streptomyces spectabilis NCBITaxon:68270	LOTUS	DOI:10.1111/J.1365-2672.2008.03788.X
Streptomyces spectabilis NCBITaxon:68270	LOTUS	DOI:10.1111/J.1574-6968.2000.TB08955.X
Streptomyces spectabilis NCBITaxon:68270	LOTUS	DOI:10.1128/JB.177.3.818-822.1995
Streptomyces spectabilis NCBITaxon:68270	LOTUS	DOI:10.7164/ANTIBIOTICS.47.1425
Streptomyces netropsis NCBITaxon:55404	LOTUS	DOI:10.1002/JOBM.200410529
Streptomyces netropsis NCBITaxon:55404	LOTUS	DOI:10.1007/S10295-019-02172-8
Streptomyces netropsis NCBITaxon:55404	LOTUS	DOI:10.1016/J.JBIOTEC.2014.01.028
Streptomyces netropsis NCBITaxon:55404	LOTUS	DOI:10.1111/J.1365-2672.2008.03788.X
Streptomyces netropsis NCBITaxon:55404	LOTUS	DOI:10.1111/J.1574-6968.2000.TB08955.X
Streptomyces netropsis NCBITaxon:55404	LOTUS	DOI:10.1128/JB.177.3.818-822.1995
Streptomyces netropsis NCBITaxon:55404	LOTUS	DOI:10.7164/ANTIBIOTICS.47.1425

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000716	Streptomyces netropsis NCBITaxon:55404	CLUSTER_UNSTATED	genbank:U70376.2

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 7

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
qHTS Assay for Inhibitors of the Human Apurinic/apyrimidinic Endonuclease 1 (APE1)	OTHER 3.5481 uM; INACTIVE	Not recorded	pubchem.aid:2517 assay qHTS Assay for Inhibitors of the Human Apurinic/apyrimidinic Endonuclease 1 (APE1) evidence reference pubchem.aid:2517 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 2517, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency. Target accession 1DE9_A was left ungrounded because PubChem did not provide a UniProtKB accession. call INACTIVE measurement type OTHER value 3.5481 units uM
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
Diffuse intrinsic pontine glioma (JHH-DIPG-1) cell line screen of MIPE4.0 library: viability qHTS assay using CellTiter-Glo	ACTIVE	Not recorded	pubchem.aid:1347062 assay Diffuse intrinsic pontine glioma (JHH-DIPG-1) cell line screen of MIPE4.0 library: viability qHTS assay using CellTiter-Glo evidence reference pubchem.aid:1347062 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1347062, deposited by 15316; assay type Confirmatory. call ACTIVE
Diffuse intrinsic pontine glioma (SU-DIPG-IV) cell line screen of MIPE4.0 library: viability qHTS assay using CellTiter-Glo	ACTIVE	Not recorded	pubchem.aid:1347063 assay Diffuse intrinsic pontine glioma (SU-DIPG-IV) cell line screen of MIPE4.0 library: viability qHTS assay using CellTiter-Glo evidence reference pubchem.aid:1347063 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1347063, deposited by 15316; assay type Confirmatory. call ACTIVE
Diffuse intrinsic pontine glioma (SU-DIPG-VI) cell line screen of MIPE4.0 library: viability qHTS assay using CellTiter-Glo	ACTIVE	Not recorded	pubchem.aid:1347066 assay Diffuse intrinsic pontine glioma (SU-DIPG-VI) cell line screen of MIPE4.0 library: viability qHTS assay using CellTiter-Glo evidence reference pubchem.aid:1347066 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1347066, deposited by 15316; assay type Confirmatory. call ACTIVE
Diffuse intrinsic pontine glioma (SU-DIPG-XIII) cell line screen of MIPE4.0 library: viability qHTS assay using CellTiter-Glo	ACTIVE	Not recorded	pubchem.aid:1347061 assay Diffuse intrinsic pontine glioma (SU-DIPG-XIII) cell line screen of MIPE4.0 library: viability qHTS assay using CellTiter-Glo evidence reference pubchem.aid:1347061 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1347061, deposited by 15316; assay type Confirmatory. call ACTIVE
High Throughput Screen to Identify Inhibitors of Mycobacterium tuberculosis H37Rv	ACTIVE	Not recorded	pubchem.aid:1332 assay High Throughput Screen to Identify Inhibitors of Mycobacterium tuberculosis H37Rv evidence reference pubchem.aid:1332 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1332, deposited by Southern Research Institute; assay type Confirmatory. call ACTIVE activity class ENZYME_INHIBITOR

Elsewhere in the fleet

AntibioticMech — CHEBI:9215 (same structure, same inchikey)

Explore across X-Mech

AntibioticMech (spectinomycin) ↗ MediaIngredientMech (CHEBI:9215) ↗ TaxonMech: Streptomyces netropsis (NCBITaxon:55404) ↗ PathwayMech (mibig:BGC0000716) ↗

Provenance

Source concept	Source	Version
BGC0000716	MIBIG	5
CHEBI:9215	CHEBI	3-star

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