NaturalProductMech

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cardol

CHEBI:2120 EXACT SEEDED

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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

Resorcinol substituted at position 5 by a pentadecyl chain.

Structure

Standard InChIKeyKVVSCMOUFCNCGX-UHFFFAOYSA-N
SMILESCCCCCCCCCCCCCCCC1=CC(=CC(=C1)O)O
Stereochemistryfully defined
Cross-referencesnpatlas:NPA008167

Filing pathway

Polyketides — 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 pks, 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.

TaxonBasisClusterEvidence
Candidatus Entotheonella sp.
NCBITaxon:2066855		 SOURCE_ASSERTION mibig:BGC0002332 DOI:10.1002/cbic.201900352

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.

TaxonSourceReference
Ardisia colorata
NCBITaxon:1009002		 LOTUS DOI:10.1248/CPB.49.1664
Ardisia colorata
NCBITaxon:1009002		 LOTUS DOI:10.1248/CPB.50.1484
Byssomerulius incarnatus
NCBITaxon:1045806		 LOTUS DOI:10.1021/NP050520D
Grevillea robusta
NCBITaxon:105748		 LOTUS DOI:10.1021/NP0605687
Anacardium occidentale
NCBITaxon:171929		 LOTUS DOI:10.1002/PTR.2650070309
Anacardium occidentale
NCBITaxon:171929		 LOTUS DOI:10.1016/0031-9422(92)83267-3
Anacardium occidentale
NCBITaxon:171929		 LOTUS DOI:10.1021/JF00002A039
Anacardium occidentale
NCBITaxon:171929		 LOTUS DOI:10.1021/JF00030A035
Anacardium occidentale
NCBITaxon:171929		 LOTUS DOI:10.1021/JF020224W
Anacardium occidentale
NCBITaxon:171929		 LOTUS DOI:10.1021/NP50106A021
Anacardium occidentale
NCBITaxon:171929		 LOTUS DOI:10.1080/10575639208048898
Streptomyces cyaneus
NCBITaxon:1904		 LOTUS DOI:10.1038/JA.2015.22
Streptomyces cyaneus
NCBITaxon:1904		 LOTUS DOI:10.7164/ANTIBIOTICS.45.886
Streptomyces cyaneus
NCBITaxon:1904		 CHEBI PMID:21462031
Ardisia gigantifolia
NCBITaxon:213405		 LOTUS DOI:10.1016/J.PHYTOCHEM.2009.04.004
Baccharis quitensis
NCBITaxon:2707514		 LOTUS DOI:10.1016/0031-9422(81)84033-2
Mangifera indica
NCBITaxon:29780		 LOTUS DOI:10.1016/0885-5765(87)90041-5
Mangifera indica
NCBITaxon:29780		 LOTUS DOI:10.1016/S0031-9422(00)81560-5
Mangifera indica
NCBITaxon:29780		 LOTUS DOI:10.1016/S0048-4059(86)80019-4
Ginkgo biloba
NCBITaxon:3311		 LOTUS DOI:10.1002/PCA.733
Ginkgo biloba
NCBITaxon:3311		 LOTUS DOI:10.1016/J.CHROMA.2009.01.013
Ginkgo biloba
NCBITaxon:3311		 LOTUS DOI:10.1515/ZNC-2000-11-1206
Ginkgo biloba
NCBITaxon:3311		 CHEBI PMID:21462031
Angelica keiskei
NCBITaxon:357850		 LOTUS DOI:10.1016/S0304-3835(03)00466-X
Hakea amplexicaulis
NCBITaxon:3815947		 LOTUS DOI:10.1021/TX00004A003

Biosynthetic gene clusters 1

AccessionHostLocus evidenceGenome
mibig:BGC0002332 Candidatus Entotheonella sp.
NCBITaxon:2066855 		CLUSTER_DEMONSTRATED genbank:MK988560.1

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.

Biosynthesis curated

Written by a curator with claim-level evidence on each step; not derived from a source. This is what the rest of the record exists to support.

StepEnzymeReactionSubstrate → productEvidence
1 AgqB native 431 reference
UniProtKB:I0HIZ0		 CHEBI:2120 → ungrounded https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000081.json

Step 1: MITE0000081-reported hydroxylation of linear-C15 cardol (CHEBI:2120) by Actinoplanes missouriensis 431 AgqB (UniProtKB:I0HIZ0, BAL92977.1, agqB/AMIS_77570 on AP012319.1, BGC0001077). Synchronizes biosynthetic_pathway with the existing MITE-backed causal_graph without upgrading producer or locus evidence grades.

Mechanism & Biosynthesis Overview

PRODUCERS & OCCURRENCE 1 producer (0 causal) 25 cited occurrences BIOSYNTHETIC LOCUS 1 gene cluster 1 curated pathway step NATURAL PRODUCT cardol CHEBI:2120 Polyketides TARGETS & BIOACTIVITY 0 molecular targets 0 bioactivities · 1 graph

Causal graph — biosynthesis 4 nodes, 3 edges

MITE-reported hydroxylation of exact linear-C15 cardol as a substrate in an alkylresorcinol tailoring context. AgqB's native Actinoplanes missouriensis 431 reference is sequence-verified. This graph consumes cardol; it does not establish cardol production by that organism. Current UniProt automated dibenzothiophene annotations are not cardol activity evidence. The owner's distinct source producer/locus and open name disagreement are retained; not full-record sign-off.

SubjectPredicateObjectNotesEvidence
AgqB native 431 reference is_database_reported_catalyst_of MITE-reported AgqB substrate hydroxylation MITE supplies functional attribution; native translation and current UniProt establish identity only. No primary assay, native cofactor occupancy, electron donor, rate, site, phenotype or complex is adopted.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000081.json
https://www.uniprot.org/uniprotkb/I0HIZ0
https://www.ncbi.nlm.nih.gov/protein/BAL92977.1
https://www.ncbi.nlm.nih.gov/nuccore/AP012319.1?from=8381000&to=8382500
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000081.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    MITE0000081 version 3, active, names AgqB/I0HIZ0/BAL92977.1 and BGC0001077. Its fourth enumerated reaction hydroxylates linear-C15 alkylresorcinol; the product is flagged intermediate. The heterologous expression code is database-level; the cited primary paper was inaccessible. This is not independently inspected primary assay evidence.
    snippet
    Hydroxylation of alkylresorcinol substrate.
  • reference
    https://www.uniprot.org/uniprotkb/I0HIZ0
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Current TrEMBL entry56/sequence1,384aa, agqB/AMIS_77570, taxon512565, inferred-from-homology existence. Direct EMBL AP012319/BAL92977.1 link and full sequence support identity. Its automated ARBA dibenzothiophene name, reactions and pathway, and predicted cofactor/domain annotations, are not independent alkylresorcinol evidence. No FUNCTION comment.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/BAL92977.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Complete independent384-residue GenPept alkylresorcinol hydroxylase reference, agqB/AMIS_77570, A.missouriensis431, NBRC102363/taxon512565; complete coded_by inspected. This reference does not establish a historical assay stock or construct.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AP012319.1?from=8381000&to=8382500
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-07
    notes
    Complete1155-nt minus-strand CDS8381171..8382325 in a forward 1501-bp genomic window8381000..8382500. Codon1/table11 translation equals native annotation, independent BAL92977.1 and current I0HIZ0, all384aa. Independent absolute coded_by coordinates map to local 172..1326 and yield identical DNA; native431/NBRC102363/taxon512565 source qualifiers match. A full-CDS window, not a full-genome read.
cardol is_database_example_substrate_of MITE-reported AgqB substrate hydroxylation The fourth MITE example substrate matches full key KVVSCMOUFCNCGX-UHFFFAOYSA-N and complete stereo in the pinned repository-helper/RDKit2026.03.5 screen. It is linear-C15 cardol, not the other branched-chain examples. The owner's existing cardol/Adipostatin-A name disagreement stays OPEN. No upstream synthesis or exact native assay substrate is inferred.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000081.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000081.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    MITE0000081 version 3, active, names AgqB/I0HIZ0/BAL92977.1 and BGC0001077. Its fourth enumerated reaction hydroxylates linear-C15 alkylresorcinol; the product is flagged intermediate. The heterologous expression code is database-level; the cited primary paper was inaccessible. This is not independently inspected primary assay evidence.
MITE-reported AgqB substrate hydroxylation has_database_example_product AgqB hydroxylated linear-C15 example product The encoded hydroxylated product is intermediate and remains externally ungrounded; it is not cardol. No downstream sequence or pathway finality is inferred. MITE's BGC0001077 and the AgqB reference organism are not transferred to the owner's source producer Candidatus Entotheonella sp./BGC0002332. Existing SOURCE_ASSERTION/CLUSTER_DEMONSTRATED grades, occurrences and SEEDED status are preserved.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000081.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000081.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    MITE0000081 version 3, active, names AgqB/I0HIZ0/BAL92977.1 and BGC0001077. Its fourth enumerated reaction hydroxylates linear-C15 alkylresorcinol; the product is flagged intermediate. The heterologous expression code is database-level; the cited primary paper was inaccessible. This is not independently inspected primary assay evidence.

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

Explore across X-Mech

AntibioticMech (cardol) ↗ MediaIngredientMech (CHEBI:2120) ↗ TaxonMech: Candidatus Entotheonella sp. (NCBITaxon:2066855) ↗ PathwayMech (mibig:BGC0002332) ↗

Open questions 1

name-disagreement — ChEBI calls this structure 'cardol' and MIBiG calls it 'Adipostatin A'. They share a Standard InChIKey, so if the names denote different compounds then one upstream record has the wrong structure. Check which.

Provenance

Source conceptSourceVersion
BGC0002332MIBIG2
CHEBI:2120CHEBI3-star

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