swainsonine

CHEBI:9367 EXACT SEEDED enzyme 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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.

An indolizidine alkaloid isolated from the plant Swainsona canescens with three hydroxy substituents at positions 1, 2 and 8.

Structure

Standard InChIKey	FXUAIOOAOAVCGD-WCTZXXKLSA-N
SMILES	C1C[C@H]([C@@H]2[C@@H]([C@@H](CN2C1)O)O)O
Stereochemistry	fully defined
Cross-references	pubchem:51683

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 nrps, pks, 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
Metarhizium robertsii ARSEF 23 NCBITaxon:655844	BGC_CHARACTERIZED	mibig:BGC0002270	PMID:32786262
Chaetothyriaceae sp. NCBITaxon:1963369	SOURCE_ASSERTION	mibig:BGC0001793	DOI:10.7150/ijbs.3882
Alternaria oxytropis NCBITaxon:570715	SOURCE_ASSERTION	mibig:BGC0001794	PMID:28381497

Occurrences 25

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
Slafractonia leguminicola NCBITaxon:1541393	LOTUS	DOI:10.1016/S0040-4020(01)97625-2
Slafractonia leguminicola NCBITaxon:1541393	LOTUS	DOI:10.1021/JA00211A039
Slafractonia leguminicola NCBITaxon:1541393	LOTUS	DOI:10.1021/JO00390A024
Slafractonia leguminicola NCBITaxon:1541393	LOTUS	DOI:10.1128/AEM.48.2.386-388.1984
Astragalus whitneyi NCBITaxon:1769941	LOTUS	DOI:10.1002/PCA.2800020307
Oxytropis riparia NCBITaxon:1938221	LOTUS	DOI:10.1002/PCA.2800020307
Astragalus flavus NCBITaxon:2014685	LOTUS	DOI:10.1002/PCA.2800020307
Astragalus bisulcatus NCBITaxon:20406	LOTUS	DOI:10.1002/PCA.2800020307
Astragalus hallii NCBITaxon:20413	LOTUS	DOI:10.1002/PCA.2800020307
Astragalus lentiginosus NCBITaxon:20416	LOTUS	DOI:10.1002/PCA.2800020307
Astragalus lentiginosus NCBITaxon:20416	LOTUS	DOI:10.1002/PCA.713
Astragalus lentiginosus NCBITaxon:20416	LOTUS	DOI:10.1021/BI00459A032
Astragalus purshii NCBITaxon:20422	LOTUS	DOI:10.1002/PCA.2800020307
Oxytropis lambertii NCBITaxon:20805	LOTUS	DOI:10.1002/PCA.2800020307
Oxytropis lambertii NCBITaxon:20805	LOTUS	DOI:10.1021/JF010596P
Castanospermum australe NCBITaxon:24962	LOTUS	DOI:10.1021/NP50069A011
Ipomoea calobra NCBITaxon:2607090	LOTUS	DOI:10.1021/NP50120A009
Astragalus pycnostachyus NCBITaxon:2897604	LOTUS	DOI:10.1002/PCA.2800020307
Astragalus emoryanus NCBITaxon:3084112	LOTUS	DOI:10.1002/PCA.2800020307
Astragalus emoryanus NCBITaxon:3084112	LOTUS	DOI:10.1104/PP.76.4.972
Fabaceae NCBITaxon:3803	LOTUS	DOI:10.1002/PCA.2800020307
Astragalus wootonii NCBITaxon:457888	LOTUS	DOI:10.1002/PCA.2800020307
Astragalus falcatus NCBITaxon:47038	LOTUS	DOI:10.1002/PCA.2800020307
Oxytropis glabra NCBITaxon:483874	LOTUS	DOI:10.1002/PCA.2800020307
Swainsona canescens NCBITaxon:491199	LOTUS	DOI:10.1016/S0021-9258(18)32772-8

Biosynthetic gene clusters 3

Accession	Host	Locus evidence	Genome
mibig:BGC0002270	Metarhizium robertsii ARSEF 23 NCBITaxon:655844	CLUSTER_DEMONSTRATED	genbank:ADNJ02000001.1
mibig:BGC0001793	Chaetothyriaceae sp. NCBITaxon:1963369	CLUSTER_UNSTATED	genbank:KY365740.1
mibig:BGC0001794	Alternaria oxytropis NCBITaxon:570715	CLUSTER_UNSTATED	genbank:KY365741.1

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 2 nodes, 1 edge

Swainsonine inhibits Drosophila Golgi alpha-mannosidase II.

Subject	Predicate	Object	Notes	Evidence
swainsonine	inhibits	Drosophila Golgi alpha-mannosidase II	PubChem BioAssay AID 1799635 maps this exact Standard InChIKey to a 3 nM Ki measurement against Drosophila Golgi alpha-mannosidase II, and Q24451 resolves in UniProtKB to the D. melanogaster alpha-Man-IIa gene product.	DOI:10.1002/cbic.200900750 reference DOI:10.1002/cbic.200900750 evidence type PRIMARY_EXPERIMENT notes Kuntz et al. characterized 5-substituted swainsonine analogue binding to the soluble catalytic domain of Drosophila GMII; the BindingDB-deposited PubChem assay reports swainsonine with Ki 0.003 uM.

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

Bioactivities 9

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
Confirmatory qHTS for small molecule stabilizers of the endoplasmic reticulum resident proteome: Secreted ER Calcium Modulated Protein (SERCaMP) assay	OTHER 0.1 uM; NOT_DETERMINED	Not recorded	PMID:33910017 assay Confirmatory qHTS for small molecule stabilizers of the endoplasmic reticulum resident proteome: Secreted ER Calcium Modulated Protein (SERCaMP) assay evidence reference PMID:33910017 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1508628, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. call NOT_DETERMINED measurement type OTHER value 0.1 units uM
Confirmatory qHTS for small molecule stabilizers of the endoplasmic reticulum resident proteome: Secreted ER Calcium Modulated Protein (SERCaMP) assay	OTHER 31.6228 uM; NOT_DETERMINED	Not recorded	PMID:33910017 assay Confirmatory qHTS for small molecule stabilizers of the endoplasmic reticulum resident proteome: Secreted ER Calcium Modulated Protein (SERCaMP) assay evidence reference PMID:33910017 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1508628, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. call NOT_DETERMINED measurement type OTHER value 31.6228 units uM
Experimentally measured binding affinity data (IC50) for protein-ligand complexes derived from PDB	IC50 0.02 uM; ACTIVE	Not recorded	PMID:11406577 assay Experimentally measured binding affinity data (IC50) for protein-ligand complexes derived from PDB evidence reference PMID:11406577 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 977608, deposited by Shanghai Institute of Organic Chemistry; assay type Other. Target accession 1HWW_A was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type IC50 value 0.02 units uM activity class ENZYME_INHIBITOR
Golgi α-Mannosidase II (alpha-hGMII) and α-Mannosidase (alpha-hLM) Activity Assay from US Patent US20240190866: "POLYHYDROXYLATED INDOLIZIDINE AND PYRROLIZIDINE DERIVATIVES AND USES THEREOF"	IC50 0.08 uM; ACTIVE	UniProtKB:O00754	pubchem.aid:1964041 assay Golgi α-Mannosidase II (alpha-hGMII) and α-Mannosidase (alpha-hLM) Activity Assay from US Patent US20240190866: "POLYHYDROXYLATED INDOLIZIDINE AND PYRROLIZIDINE DERIVATIVES AND USES THEREOF" evidence reference pubchem.aid:1964041 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1964041, deposited by BindingDB; assay type Confirmatory. call ACTIVE measurement type IC50 value 0.08 units uM target enzyme UniProtKB:O00754
Golgi α-Mannosidase II (alpha-hGMII) and α-Mannosidase (alpha-hLM) Activity Assay from US Patent US20240190866: "POLYHYDROXYLATED INDOLIZIDINE AND PYRROLIZIDINE DERIVATIVES AND USES THEREOF"	IC50 0.04 uM; ACTIVE	UniProtKB:Q16706	pubchem.aid:1964041 assay Golgi α-Mannosidase II (alpha-hGMII) and α-Mannosidase (alpha-hLM) Activity Assay from US Patent US20240190866: "POLYHYDROXYLATED INDOLIZIDINE AND PYRROLIZIDINE DERIVATIVES AND USES THEREOF" evidence reference pubchem.aid:1964041 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1964041, deposited by BindingDB; assay type Confirmatory. call ACTIVE measurement type IC50 value 0.04 units uM target enzyme UniProtKB:Q16706
Inhibition Assay from Article 10.1002/cbic.200900750: "Structural investigation of the binding of 5-substituted swainsonine analogues to Golgi alpha-mannosidase II."	KI 0.003 uM; ACTIVE	UniProtKB:Q24451	PMID:20209559 assay Inhibition Assay from Article 10.1002/cbic.200900750: "Structural investigation of the binding of 5-substituted swainsonine analogues to Golgi alpha-mannosidase II." evidence reference PMID:20209559 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1799635, deposited by BindingDB; assay type Confirmatory. call ACTIVE measurement type KI value 0.003 units uM target enzyme UniProtKB:Q24451 activity class ENZYME_INHIBITOR
Primary qHTS for delayed death inhibitors of the malarial parasite plastid, 96 hour incubation	OTHER 9.5283 uM; ACTIVE	Not recorded	pubchem.aid:504834 assay Primary qHTS for delayed death inhibitors of the malarial parasite plastid, 96 hour incubation evidence reference pubchem.aid:504834 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 504834, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency. call ACTIVE measurement type OTHER value 9.5283 units uM activity class ENZYME_INHIBITOR
qHTS assay for identifying genotoxic compounds that show differential cytotoxicity against isogenic chicken DT40 cell lines with known DNA damage response pathways - Rev3 mutant cell line	OTHER 26.6032 uM; NOT_DETERMINED	Not recorded	pubchem.aid:743014 assay qHTS assay for identifying genotoxic compounds that show differential cytotoxicity against isogenic chicken DT40 cell lines with known DNA damage response pathways - Rev3 mutant cell line evidence reference pubchem.aid:743014 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 743014, deposited by 824; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. call NOT_DETERMINED measurement type OTHER value 26.6032 units uM
Experimentally measured binding affinity data derived from PDB	ACTIVE	Not recorded	PMID:11406577 assay Experimentally measured binding affinity data derived from PDB evidence reference PMID:11406577 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1811, deposited by Shanghai Institute of Organic Chemistry; assay type Other. Target accession 1HWW_A was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE activity class ENZYME_INHIBITOR

Explore across X-Mech

AntibioticMech (swainsonine) ↗ MediaIngredientMech (CHEBI:9367) ↗ TaxonMech: Metarhizium robertsii ARSEF 23 (NCBITaxon:655844) ↗ TaxonMech: Chaetothyriaceae sp. (NCBITaxon:1963369) ↗ TaxonMech: Alternaria oxytropis (NCBITaxon:570715) ↗ PathwayMech (mibig:BGC0002270) ↗ PathwayMech (mibig:BGC0001793) ↗ PathwayMech (mibig:BGC0001794) ↗

Open questions 1

shared-structure — This structure is reported by more than one MIBiG entry: BGC0001793, BGC0001794, BGC0002270. Confirm they describe the same compound rather than an upstream cross-reference error.

Provenance

Source concept	Source	Version
BGC0002270	MIBIG	2
BGC0001793	MIBIG	4
BGC0001794	MIBIG	4
CHEBI:9367	CHEBI	3-star

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