apicidin
naturalproductmech:mibig-f6e5a95e78 MINTED SEEDED antiparasiticcytotoxic
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.
Causal graph — bioactivity 5 nodes, 4 edges
Apicidin inhibits human histone deacetylases HDAC1, HDAC3, HDAC4, and HDAC6.
| Subject | Predicate | Object | Evidence |
|---|---|---|---|
| apicidin | inhibits | human histone deacetylase 1 | DOI:10.1016/j.bmcl.2008.02.025 |
| apicidin | inhibits | human histone deacetylase 3 | DOI:10.1016/j.bmcl.2008.02.025 |
| apicidin | inhibits | human histone deacetylase 4 | DOI:10.1016/j.bmcl.2008.02.025 |
| apicidin | inhibits | human histone deacetylase 6 | DOI:10.1016/j.bmcl.2008.02.025 |
Every edge carries its own citation; an uncited edge is refused by the corpus tests.
Causal graph — bioactivity 2 nodes, 1 edges
Apicidin inhibits recombinant Plasmodium falciparum 3D7 pfHDAC-1.
| Subject | Predicate | Object | Evidence |
|---|---|---|---|
| apicidin | inhibits | Plasmodium falciparum 3D7 histone deacetylase 1 | DOI:10.1021/jm801654y |
Every edge carries its own citation; an uncited edge is refused by the corpus tests.
Bioactivities 7
| Assay | Result | Reference |
|---|---|---|
| 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 | PMID:18308563 |
| 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 | PMID:18308563 |
| 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 | PMID:18308563 |
| 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 | PMID:18308563 |
| 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 | PMID:18308563 |
| 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 | PMID:18370373 |
| 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 | PMID:19317450 |
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.