aphidicolin

CHEBI:2766 ·resolve ·ANTIVIRAL ·EXACT SEEDED

A tetracyclic diterpenoid that has an tetradecahydro-8,11a-methanocyclohepta[a]naphthalene skeleton with two hydroxymethyl substituents at positions 4 and 9, two methyl substituents at positions 4 and 11b and two hydroxy substituents at positions 3 and 9. An antibiotic with antiviral and antimitotical properties. Aphidicolin is a reversible inhibitor of eukaryotic nuclear DNA replication. — ChEBI

Machine-generated and unreviewed. Identity, structure and cross-references come straight from ChEBI's and CARD's own data; no curator has signed off on this record yet.

Classification

Strictly broader compounds or drug classes this molecule belongs to.

Label unavailable CHEBI:52557

Chemical structure

Computed structure properties
Molecular formula	C20H34O4
Charge	0
Average mass	338.488 Da
Monoisotopic mass	338.24571 Da
Source	ChEBI
InChIKey	NOFOAYPPHIUXJR-APNQCZIXSA-N

SMILES

[H][C@@]12CC[C@]3([H])[C@](C)(CC[C@@H](O)[C@@]3(C)CO)[C@]13CC[C@](O)(CO)[C@H](C2)C3

InChI

InChI=1S/C20H34O4/c1-17(11-21)15-4-3-13-9-14-10-19(13,7-8-20(14,24)12-22)18(15,2)6-5-16(17)23/h13-16,21-24H,3-12H2,1-2H3/t13-,14+,15-,16+,17-,18-,19-,20-/m0/s1

Also called

(3R,4R,4aR,6aS,8R,9R,11aS,11bS)-4,9-bis(hydroxymethyl)-4,11b-dimethyltetradecahydro-8,11a-methanocyclohepta[a]naphthalene-3,9-diol (EXACT_SYNONYM)— chebi
(3α,4α,5α,17α)-3,17-dihydroxy-4-methyl-9,15-cyclo-C,18-dinor-14,15-secoandrostane-4,17-dimethanol (EXACT_SYNONYM)— chebi
Aphidicolin (EXACT_SYNONYM)— chebi
aphidocolin (EXACT_SYNONYM)— chebi

Cross-references

Identifiers for this same structure in other resources. An accession that lands on two different structures in this corpus is withheld from both rather than shown here, since it names at most one of them.

Patents and articles

Documents about this compound. A patent covers a class and an article covers a topic; neither identifies a structure.

Activity roles

Every antimicrobial role a source asserts for this compound — the unreduced evidence behind its antimicrobial_class.

antimicrobial agent CHEBI:33281
antiviral drug CHEBI:36044

Source concepts

Every upstream concept that resolved to this record. The merge is the product: this is what shows ChEBI and CARD are describing the same structure.

Upstream concepts merged into this record
Source	Native ID	Label	Minted CURIE	Version
CHEBI	`CHEBI:2766`	aphidicolin	`antibioticmech:chebi-78bb6a4be0`	2026-08-30

Mechanism summary

Mode of action: NUCLEIC_ACID_SYNTHESIS_INHIBITION host shared target — Assigned from ChEBI role CHEBI:59517 (DNA synthesis inhibitor). ChEBI asserts the role on the compound. The target it names is one the host has too, so the mechanism is true but is not evidence of selectivity — see mode_of_action_target_scope. Not a curator's mechanistic review.

Producer organisms

Organisms that biosynthesize this compound. Cluster link evidence is how the upstream source graded the gene cluster, so it is populated only for a source that grades it. An empty cell is not weaker support: a curator-authored producer carries its support in Evidence instead. Where the source entry named several compounds, the evidence is marked inherited, meaning it covers this compound together with the cluster's other products rather than singling it out. Those products need not be related to each other: a cluster can list an intermediate, a precursor and a finished antibiotic side by side.

Producer organisms
Organism	BGC	Cluster link evidence	Source	Quality	Note	Evidence
Phoma betae NCBITaxon:1979465	BGC0000676	Heterologous expression cluster inherited	MIBIG 4.0.1 (entry 5)	questionable	MIBiG active entry; compound 'aphidicolin' joined by exact Standard InChIKey.	PMID:14745177 (MIBiG's first legacy reference for the entry, inherited rather than attached to the compound. It supports that the entry exists; it is NOT established as evidence for this specific producer/compound link.)

Curation history

SEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Seeded from data/raw/ inventories (CHEBI)
RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-09-08 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-09-08 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-09-10 · seed_from_sources
Re-seeded from updated data/raw/ inventories

Provenance

Seeded by scripts/seed_from_sources.py from the committed inventories in data/raw/. View the record (YAML).

Explore across X-Mech: MediaIngredientMech (aphidicolin) · CultureMech · NaturalProductMech · PathwayMech · TraitMech · TaxonMech (Phoma betae)