apicidin

naturalproductmech:mibig-f6e5a95e78 MINTED SEEDED antiparasiticcytotoxic

Grounding review: No 3-star ChEBI entry shares this structure, so the record keeps a content-hashed identifier.

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	JWOGUUIOCYMBPV-LQJYRIKDSA-N
SMILES	[H][C@]12CCCCN1C(=O)[C@@H](NC(=O)[C@H](CC1=CN(OC)C3=C1C=CC=C3)NC(=O)[C@H](CCCCCC(=O)CC)NC2=O)C(C)CC
Stereochemistry	undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers
Cross-references	npatlas:NPA013880, pubchem:467801

Filing pathway

Amino acids and peptides — 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, 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
Fusarium incarnatum NCBITaxon:298378	SOURCE_ASSERTION	mibig:BGC0000304	DOI:10.1073/pnas.93.23.13143

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
Fusarium incarnatum NCBITaxon:1894967	LOTUS	DOI:10.1111/J.1365-2958.2010.07109.X

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000304	Fusarium incarnatum NCBITaxon:298378	CLUSTER_UNSTATED	genbank:GQ331953.1

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 5 nodes, 4 edges

Apicidin inhibits human histone deacetylases HDAC1, HDAC3, HDAC4, and HDAC6.

Subject	Predicate	Object	Notes	Evidence
apicidin	inhibits	human histone deacetylase 1	BindingDB maps this exact Standard InChIKey to active 23 and 44 nM IC50 measurements against human HDAC1, and Q13547 resolves in UniProtKB to the human HDAC1 gene product.	DOI:10.1016/j.bmcl.2008.02.025 DOI:10.1021/jm800079s reference DOI:10.1016/j.bmcl.2008.02.025 evidence type PRIMARY_EXPERIMENT notes PubChem BioAssay AID 1798526 was deposited by BindingDB for PMID 18308563 and reports active apicidin inhibition of human HDAC1. reference DOI:10.1021/jm800079s evidence type PRIMARY_EXPERIMENT notes PubChem BioAssay AID 1798524 was deposited by BindingDB for PMID 18370373 and reports active apicidin inhibition of human HDAC1.
apicidin	inhibits	human histone deacetylase 3	BindingDB maps this exact Standard InChIKey to a 9.7 nM IC50 measurement against human HDAC3, and O15379 resolves in UniProtKB to the human HDAC3 gene product.	DOI:10.1016/j.bmcl.2008.02.025 reference DOI:10.1016/j.bmcl.2008.02.025 evidence type PRIMARY_EXPERIMENT notes PubChem BioAssay AID 1798526 was deposited by BindingDB for PMID 18308563 and reports active apicidin inhibition of human HDAC3.
apicidin	inhibits	human histone deacetylase 4	BindingDB maps this exact Standard InChIKey to active 3.6 and 8.7 uM IC50 measurements against human HDAC4, and P56524 resolves in UniProtKB to the human HDAC4 gene product.	DOI:10.1016/j.bmcl.2008.02.025 reference DOI:10.1016/j.bmcl.2008.02.025 evidence type PRIMARY_EXPERIMENT notes PubChem BioAssay AID 1798526 was deposited by BindingDB for PMID 18308563 and reports active apicidin inhibition of human HDAC4.
apicidin	inhibits	human histone deacetylase 6	BindingDB maps this exact Standard InChIKey to a 4.3 uM IC50 measurement against human HDAC6, and Q9UBN7 resolves in UniProtKB to the human HDAC6 gene product.	DOI:10.1016/j.bmcl.2008.02.025 reference DOI:10.1016/j.bmcl.2008.02.025 evidence type PRIMARY_EXPERIMENT notes PubChem BioAssay AID 1798526 was deposited by BindingDB for PMID 18308563 and reports active apicidin inhibition of human HDAC6.

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

Causal graph — bioactivity 2 nodes, 1 edge

Apicidin inhibits recombinant Plasmodium falciparum 3D7 pfHDAC-1.

Subject	Predicate	Object	Notes	Evidence
apicidin	inhibits	Plasmodium falciparum 3D7 histone deacetylase 1	BindingDB-deposited PubChem BioAssay AID 1799021 maps this exact Standard InChIKey to an active 0.001 uM IC50 measurement in a recombinant pfHDAC-1 enzyme assay; the source paper identifies pfHDAC-1 as historical PlasmoDB locus PFI1260c, and Q7K6A1 resolves in UniProtKB to Plasmodium falciparum 3D7 PF3D7_0925700.	DOI:10.1021/jm801654y reference DOI:10.1021/jm801654y evidence type PRIMARY_EXPERIMENT notes PubChem BioAssay AID 1799021 was deposited by BindingDB for PMID 19317450 and reports an active apicidin IC50 value in the PfHDAC-1 enzyme assay.

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

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
HDAC Activity Assay from Article 10.1016/j.bmcl.2008.02.025: "Probing the elusive catalytic activity of vertebrate class IIa histone deacetylases."	IC50 0.0097 uM; ACTIVE	UniProtKB:O15379	PMID:18308563 assay HDAC Activity Assay from Article 10.1016/j.bmcl.2008.02.025: "Probing the elusive catalytic activity of vertebrate class IIa histone deacetylases." evidence reference PMID:18308563 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1798526, deposited by BindingDB; assay type Confirmatory. call ACTIVE measurement type IC50 value 0.0097 units uM target enzyme UniProtKB:O15379
HDAC Activity Assay from Article 10.1016/j.bmcl.2008.02.025: "Probing the elusive catalytic activity of vertebrate class IIa histone deacetylases."	IC50 3.6 uM; ACTIVE	UniProtKB:P56524	PMID:18308563 assay HDAC Activity Assay from Article 10.1016/j.bmcl.2008.02.025: "Probing the elusive catalytic activity of vertebrate class IIa histone deacetylases." evidence reference PMID:18308563 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1798526, deposited by BindingDB; assay type Confirmatory. call ACTIVE measurement type IC50 value 3.6 units uM target enzyme UniProtKB:P56524
HDAC Activity Assay from Article 10.1016/j.bmcl.2008.02.025: "Probing the elusive catalytic activity of vertebrate class IIa histone deacetylases."	IC50 8.7 uM; ACTIVE	UniProtKB:P56524	PMID:18308563 assay HDAC Activity Assay from Article 10.1016/j.bmcl.2008.02.025: "Probing the elusive catalytic activity of vertebrate class IIa histone deacetylases." evidence reference PMID:18308563 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1798526, deposited by BindingDB; assay type Confirmatory. call ACTIVE measurement type IC50 value 8.7 units uM target enzyme UniProtKB:P56524
HDAC Activity Assay from Article 10.1016/j.bmcl.2008.02.025: "Probing the elusive catalytic activity of vertebrate class IIa histone deacetylases."	IC50 0.023 uM; ACTIVE	UniProtKB:Q13547	PMID:18308563 assay HDAC Activity Assay from Article 10.1016/j.bmcl.2008.02.025: "Probing the elusive catalytic activity of vertebrate class IIa histone deacetylases." evidence reference PMID:18308563 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1798526, deposited by BindingDB; assay type Confirmatory. call ACTIVE measurement type IC50 value 0.023 units uM target enzyme UniProtKB:Q13547
HDAC Activity Assay from Article 10.1016/j.bmcl.2008.02.025: "Probing the elusive catalytic activity of vertebrate class IIa histone deacetylases."	IC50 4.3 uM; ACTIVE	UniProtKB:Q9UBN7	PMID:18308563 assay HDAC Activity Assay from Article 10.1016/j.bmcl.2008.02.025: "Probing the elusive catalytic activity of vertebrate class IIa histone deacetylases." evidence reference PMID:18308563 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1798526, deposited by BindingDB; assay type Confirmatory. call ACTIVE measurement type IC50 value 4.3 units uM target enzyme UniProtKB:Q9UBN7
HDAC Activity Assay from Article 10.1021/jm800079s: "A novel series of potent and selective ketone histone deacetylase inhibitors with antitumor activity in vivo."	IC50 0.044 uM; ACTIVE	UniProtKB:Q13547	PMID:18370373 assay HDAC Activity Assay from Article 10.1021/jm800079s: "A novel series of potent and selective ketone histone deacetylase inhibitors with antitumor activity in vivo." evidence reference PMID:18370373 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1798524, deposited by BindingDB; assay type Confirmatory. call ACTIVE measurement type IC50 value 0.044 units uM target enzyme UniProtKB:Q13547 activity class CYTOTOXIC
pfHDAC-1 Enzyme Assay from Article 10.1021/jm801654y: "Identification and characterization of small molecule inhibitors of a class I histone deacetylase from Plasmodium falciparum."	IC50 0.001 uM; ACTIVE	Not recorded	PMID:19317450 assay pfHDAC-1 Enzyme Assay from Article 10.1021/jm801654y: "Identification and characterization of small molecule inhibitors of a class I histone deacetylase from Plasmodium falciparum." evidence reference PMID:19317450 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1799021, deposited by BindingDB; assay type Confirmatory. call ACTIVE measurement type IC50 value 0.001 units uM activity class ANTIPARASITIC

Explore across X-Mech

AntibioticMech (apicidin) ↗ MediaIngredientMech (naturalproductmech:mibig-f6e5a95e78) ↗ TaxonMech: Fusarium incarnatum (NCBITaxon:298378) ↗ PathwayMech (mibig:BGC0000304) ↗

Provenance

Source concept	Source	Version
BGC0000304	MIBIG	4

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