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(R)-nephthenol

CHEBI:82799 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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.

A cembrane diterpenoid obtained by regio- and stereoselective hydration of the exocyclic double bond of cembrene C.

Structure

Standard InChIKeyZJWQYSDAWSDJRA-QPHFJTKNSA-N
SMILESC/C/1=C\CC/C(=C/C[C@@H](CC/C(=C/CC1)/C)C(C)(C)O)/C
Stereochemistryfully defined
Cross-referencespubchem:6443020

Filing pathway

Terpenoids — 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 terpene, 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
Stereum hirsutum FP-91666 SS1
NCBITaxon:721885		 SOURCE_ASSERTION mibig:BGC0002219 PMID:30905831

Occurrences 6

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
Sarcophyton trocheliophorum
NCBITaxon:205097		 LOTUS DOI:10.1021/JO00334A036
Litophyton arboreum
NCBITaxon:2969260		 LOTUS DOI:10.1002/CBDV.201000016
Sinularia erecta
NCBITaxon:3286376		 LOTUS DOI:10.1021/NP9705064
Sinularia ovispiculata
NCBITaxon:3286446		 LOTUS DOI:10.1021/NP50101A024
Guarea kunthiana
NCBITaxon:485821		 LOTUS DOI:10.1590/S0103-50532004000500025
Sarcophyton glaucum
NCBITaxon:70919		 LOTUS DOI:10.1248/CPB.37.631

Biosynthetic gene clusters 1

AccessionHostLocus evidenceGenome
mibig:BGC0002219 Stereum hirsutum FP-91666 SS1
NCBITaxon:721885 		CLUSTER_DEMONSTRATED genbank:JH687388.1

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 SteTC1
NCBIProtein:EIM84824.1		 RHEA:42992 CHEBI:58756 → CHEBI:82799 DOI:10.1016/j.fgb.2019.03.007

Step 1: SteTC1 cyclizes (2E,6E,10E)-geranylgeranyl diphosphate to (R)-nephthenol. The assayed Stereum hirsutum FP-91666 SS1 protein is tracked by GenPept EIM84824.1, provisional RefSeq XP_007305993.1, locus tag STEHIDRAFT_122776, and JGI model Stehi1_122776; enzyme_id is grounded to the native GenPept accession NCBIProtein:EIM84824.1 because UniParc UPI0004449431 archives the exact 316-aa sequence (RefSeq XP_007305993.1 / STEHIDRAFT_122776) without any UniProtKB entry.

Mechanism & Biosynthesis Overview

PRODUCERS & OCCURRENCE 1 producer (0 causal) 6 cited occurrences BIOSYNTHETIC LOCUS 1 gene cluster 1 curated pathway step NATURAL PRODUCT (R)-nephthenol CHEBI:82799 Terpenoids TARGETS & BIOACTIVITY 0 molecular targets 0 bioactivities · 1 graph

Causal graph — biosynthesis 3 nodes, 2 edges

Stereum hirsutum (R)-nephthenol biosynthesis graph for SteTC1-catalyzed cyclization of (2E,6E,10E)-geranylgeranyl diphosphate to (R)-nephthenol.

SubjectPredicateObjectNotesEvidence
(2E,6E,10E)-geranylgeranyl diphosphate is cyclized by SteTC1
DOI:10.1016/j.fgb.2019.03.007
mibig:BGC0002219
https://www.ncbi.nlm.nih.gov/protein/EIM84824.1
https://www.ncbi.nlm.nih.gov/protein/XP_007305993.1
https://www.uniprot.org/uniparc/UPI0004449431
  • reference
    DOI:10.1016/j.fgb.2019.03.007
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    first fungal cembrane diterpene synthase
    notes
    Li et al. functionally characterized Stereum hirsutum SteTC1 as a cembrane diterpene synthase.
  • reference
    mibig:BGC0002219
    evidence type
    DATABASE_ASSERTION
    notes
    MIBiG BGC0002219 links the Stereum hirsutum FP-91666 SS1 locus on GenBank JH687388.1 to (-)-(R)-nephthenol by heterologous expression.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/EIM84824.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    notes
    NCBI resolves GenPept EIM84824.1 to the JH687388.1 coding sequence, locus tag STEHIDRAFT_122776, and JGI model Stehi1_122776.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/XP_007305993.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    notes
    NCBI resolves Stereum hirsutum XP_007305993.1 to locus tag STEHIDRAFT_122776 and JGI model Stehi1_122776, and describes it as a provisional RefSeq identical to GenPept EIM84824.1.
  • reference
    https://www.uniprot.org/uniparc/UPI0004449431
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-23
    snippet
    XP_007305993.1
    notes
    UniParc UPI0004449431 archives the exact 316-aa Stereum hirsutum FP-91666 SS1 STEHIDRAFT_122776 protein sequence (RefSeq XP_007305993.1, identical to GenPept EIM84824.1 on JH687388.1) with a RefSeq cross-reference only and no UniProtKB entry.
SteTC1 forms (R)-nephthenol
DOI:10.1016/j.fgb.2019.03.007
mibig:BGC0002219
https://www.ncbi.nlm.nih.gov/protein/EIM84824.1
https://www.ncbi.nlm.nih.gov/protein/XP_007305993.1
https://www.uniprot.org/uniparc/UPI0004449431
  • reference
    DOI:10.1016/j.fgb.2019.03.007
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    first fungal cembrane diterpene synthase
    notes
    Li et al. functionally characterized Stereum hirsutum SteTC1 as a cembrane diterpene synthase.
  • reference
    mibig:BGC0002219
    evidence type
    DATABASE_ASSERTION
    notes
    MIBiG BGC0002219 links the Stereum hirsutum FP-91666 SS1 locus on GenBank JH687388.1 to (-)-(R)-nephthenol by heterologous expression.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/EIM84824.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    notes
    NCBI resolves GenPept EIM84824.1 to the JH687388.1 coding sequence, locus tag STEHIDRAFT_122776, and JGI model Stehi1_122776.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/XP_007305993.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    notes
    NCBI resolves Stereum hirsutum XP_007305993.1 to locus tag STEHIDRAFT_122776 and JGI model Stehi1_122776, and describes it as a provisional RefSeq identical to GenPept EIM84824.1.
  • reference
    https://www.uniprot.org/uniparc/UPI0004449431
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-23
    snippet
    XP_007305993.1
    notes
    UniParc UPI0004449431 archives the exact 316-aa Stereum hirsutum FP-91666 SS1 STEHIDRAFT_122776 protein sequence (RefSeq XP_007305993.1, identical to GenPept EIM84824.1 on JH687388.1) with a RefSeq cross-reference only and no UniProtKB entry.

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

Explore across X-Mech

AntibioticMech ((R)-nephthenol) ↗ MediaIngredientMech (CHEBI:82799) ↗ TaxonMech: Stereum hirsutum FP-91666 SS1 (NCBITaxon:721885) ↗ PathwayMech (mibig:BGC0002219) ↗

Provenance

Source conceptSourceVersion
BGC0002219MIBIG2
CHEBI:82799CHEBI3-star

This page is generated from data/natural_products/terpenoids/r-nephthenol.yaml, which is generated from the committed inventories. Neither is edited by hand.