sodorifen

naturalproductmech:mibig-0ea28266f1 MINTED SEEDED

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	GXPHTJFKVOCWKQ-PDLCYRHZSA-N
SMILES	C[C@@H]1C(=C)[C@@H]([C@@]2(C([C@]1(C(=C2C)C)C)C)C)C
Stereochemistry	undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers
Cross-references	pubchem:46187193, npatlas:NPA031220

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 2

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
Serratia plymuthica 4Rx13 NCBITaxon:682634	BGC_CHARACTERIZED	mibig:BGC0001361	PMID:27231241
Serratia plymuthica NCBITaxon:82996	SOURCE_ASSERTION	mibig:BGC0002283	PMID:30732610

Occurrences 2

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
Serratia odorifera NCBITaxon:618	LOTUS	DOI:10.1002/ANIE.200905680
Serratia plymuthica NCBITaxon:82996	LOTUS	DOI:10.1093/FEMSLE/FNW139

Biosynthetic gene clusters 2

Accession	Host	Locus evidence	Genome
mibig:BGC0001361	Serratia plymuthica 4Rx13 NCBITaxon:682634	CLUSTER_DEMONSTRATED	genbank:CP006250.1
mibig:BGC0002283	Serratia plymuthica NCBITaxon:82996	CLUSTER_DEMONSTRATED	genbank:RBLL01000001.1

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.

Step	Enzyme	Reaction	Substrate → product	Evidence
1	SodC SAM-dependent C-methyltransferase and cyclase NCBIProtein:AGO55050.1		CHEBI:175763 + CHEBI:59789 → ungrounded	DOI:10.1021/jacs.8b08510
2	SodD terpene cyclase NCBIProtein:AGO55049.1		ungrounded → naturalproductmech:mibig-0ea28266f1	DOI:10.1021/jacs.8b08510

Step 1: SodC methylates and cyclizes (2E,6E)-farnesyl diphosphate to pre-sodorifen diphosphate. The exact intermediate is left out of the structured product field because no exact stable chemical CURIE was selected. SodC enzyme_id is grounded to the native GenPept accession NCBIProtein:AGO55050.1 (UniParc UPI0001BED050 maps only to retired/obsolete UniProtKB/TrEMBL entries A0A318P5Q0.1, D1RQI8.1, and S0AH05.1).

Step 2: SodD consumes pre-sodorifen diphosphate to form sodorifen. The intermediate is left out of the structured substrate field because no exact stable chemical CURIE was selected. SodD enzyme_id is grounded to the native GenPept accession NCBIProtein:AGO55049.1 (UniParc UPI0001BED04F maps only to retired/obsolete UniProtKB/TrEMBL entries S0AGG1.1, A0A318P116.1, and D1RQI7.1).

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 6 nodes, 5 edges

Serratia plymuthica 4Rx13 SodC and SodD convert (2E,6E)-farnesyl diphosphate and S-adenosyl-L-methionine into sodorifen through pre-sodorifen diphosphate.

Subject	Predicate	Object	Evidence
(2E,6E)-farnesyl diphosphate	is methylated and cyclized by	SodC	DOI:10.1021/jacs.8b08510 https://mibig.secondarymetabolites.org/repository/BGC0001361.3/BGC0001361.gbk https://www.ncbi.nlm.nih.gov/protein/AGO55050.1 https://www.uniprot.org/uniparc/UPI0001BED050 reference DOI:10.1021/jacs.8b08510 evidence type PRIMARY_EXPERIMENT snippet Methylation and Cyclization of MEP-Derived Farnesyl Pyrophosphate notes von Reuss et al. reconstituted Serratia plymuthica 4Rx13 SodC in vitro and placed the SAM-dependent C-methyltransferase upstream of SodD in the conversion of (2E,6E)-farnesyl diphosphate toward pre-sodorifen diphosphate. reference https://mibig.secondarymetabolites.org/repository/BGC0001361.3/BGC0001361.gbk evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes MIBiG BGC0001361.3 places the Serratia plymuthica 4Rx13 SOD_c20760 CDS at complement(11196..12173) in the BGC GenBank row with protein_id AGO55050.1. reference https://www.ncbi.nlm.nih.gov/protein/AGO55050.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes NCBI GenPept AGO55050.1 is the Serratia plymuthica 4Rx13 SOD_c20760 sequence assigned here to SodC; no UniProtKB entry resolved for this accession or locus. reference https://www.uniprot.org/uniparc/UPI0001BED050 evidence type DATABASE_ASSERTION retrieved on 2026-10-23 snippet AGO55050.1 notes UniParc UPI0001BED050 archives the exact 325-aa Serratia plymuthica 4Rx13 SodC sequence (EMBL CP006250.1 protein AGO55050.1, locus tag SOD_c20760) and records that UniProtKB/TrEMBL entries A0A318P5Q0.1, D1RQI8.1, and S0AH05.1 are inactive/obsolete, confirming no active UniProtKB accession resolves for AGO55050.1.
S-adenosyl-L-methionine zwitterion	is used by	SodC	DOI:10.1021/jacs.8b08510 https://mibig.secondarymetabolites.org/repository/BGC0001361.3/BGC0001361.gbk https://www.ncbi.nlm.nih.gov/protein/AGO55050.1 https://www.uniprot.org/uniparc/UPI0001BED050 reference DOI:10.1021/jacs.8b08510 evidence type PRIMARY_EXPERIMENT snippet Methylation and Cyclization of MEP-Derived Farnesyl Pyrophosphate notes von Reuss et al. reconstituted Serratia plymuthica 4Rx13 SodC in vitro and placed the SAM-dependent C-methyltransferase upstream of SodD in the conversion of (2E,6E)-farnesyl diphosphate toward pre-sodorifen diphosphate. reference https://mibig.secondarymetabolites.org/repository/BGC0001361.3/BGC0001361.gbk evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes MIBiG BGC0001361.3 places the Serratia plymuthica 4Rx13 SOD_c20760 CDS at complement(11196..12173) in the BGC GenBank row with protein_id AGO55050.1. reference https://www.ncbi.nlm.nih.gov/protein/AGO55050.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes NCBI GenPept AGO55050.1 is the Serratia plymuthica 4Rx13 SOD_c20760 sequence assigned here to SodC; no UniProtKB entry resolved for this accession or locus. reference https://www.uniprot.org/uniparc/UPI0001BED050 evidence type DATABASE_ASSERTION retrieved on 2026-10-23 snippet AGO55050.1 notes UniParc UPI0001BED050 archives the exact 325-aa Serratia plymuthica 4Rx13 SodC sequence (EMBL CP006250.1 protein AGO55050.1, locus tag SOD_c20760) and records that UniProtKB/TrEMBL entries A0A318P5Q0.1, D1RQI8.1, and S0AH05.1 are inactive/obsolete, confirming no active UniProtKB accession resolves for AGO55050.1.
SodC	forms	pre-sodorifen diphosphate	DOI:10.1021/jacs.8b08510 https://mibig.secondarymetabolites.org/repository/BGC0001361.3/BGC0001361.gbk https://www.ncbi.nlm.nih.gov/protein/AGO55050.1 https://www.uniprot.org/uniparc/UPI0001BED050 reference DOI:10.1021/jacs.8b08510 evidence type PRIMARY_EXPERIMENT snippet Methylation and Cyclization of MEP-Derived Farnesyl Pyrophosphate notes von Reuss et al. reconstituted Serratia plymuthica 4Rx13 SodC in vitro and placed the SAM-dependent C-methyltransferase upstream of SodD in the conversion of (2E,6E)-farnesyl diphosphate toward pre-sodorifen diphosphate. reference https://mibig.secondarymetabolites.org/repository/BGC0001361.3/BGC0001361.gbk evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes MIBiG BGC0001361.3 places the Serratia plymuthica 4Rx13 SOD_c20760 CDS at complement(11196..12173) in the BGC GenBank row with protein_id AGO55050.1. reference https://www.ncbi.nlm.nih.gov/protein/AGO55050.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes NCBI GenPept AGO55050.1 is the Serratia plymuthica 4Rx13 SOD_c20760 sequence assigned here to SodC; no UniProtKB entry resolved for this accession or locus. reference https://www.uniprot.org/uniparc/UPI0001BED050 evidence type DATABASE_ASSERTION retrieved on 2026-10-23 snippet AGO55050.1 notes UniParc UPI0001BED050 archives the exact 325-aa Serratia plymuthica 4Rx13 SodC sequence (EMBL CP006250.1 protein AGO55050.1, locus tag SOD_c20760) and records that UniProtKB/TrEMBL entries A0A318P5Q0.1, D1RQI8.1, and S0AH05.1 are inactive/obsolete, confirming no active UniProtKB accession resolves for AGO55050.1.
pre-sodorifen diphosphate	is cyclized by	SodD	DOI:10.1021/jacs.8b08510 DOI:10.1093/femsle/fnw139 https://mibig.secondarymetabolites.org/repository/BGC0001361.3/BGC0001361.gbk https://www.ncbi.nlm.nih.gov/protein/AGO55049.1 https://www.uniprot.org/uniparc/UPI0001BED04F reference DOI:10.1021/jacs.8b08510 evidence type PRIMARY_EXPERIMENT snippet Methylation and Cyclization of MEP-Derived Farnesyl Pyrophosphate notes von Reuss et al. reconstituted Serratia plymuthica 4Rx13 SodD in vitro and placed the terpene cyclase downstream of SodC in the conversion of pre-sodorifen diphosphate to sodorifen. reference DOI:10.1093/femsle/fnw139 evidence type PRIMARY_EXPERIMENT notes Domik et al. assigned SOD_c20750 to the four-gene sodorifen biosynthetic cluster and used knockouts in Serratia plymuthica 4Rx13 to support its role in sodorifen production. reference https://mibig.secondarymetabolites.org/repository/BGC0001361.3/BGC0001361.gbk evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes MIBiG BGC0001361.3 places the Serratia plymuthica 4Rx13 SOD_c20750 CDS at complement(10001..11155) in the BGC GenBank row with protein_id AGO55049.1. reference https://www.ncbi.nlm.nih.gov/protein/AGO55049.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes NCBI GenPept AGO55049.1 is the Serratia plymuthica 4Rx13 SOD_c20750 sequence assigned here to SodD; no UniProtKB entry resolved for this accession or locus. reference https://www.uniprot.org/uniparc/UPI0001BED04F evidence type DATABASE_ASSERTION retrieved on 2026-10-23 snippet AGO55049.1 notes UniParc UPI0001BED04F archives the exact 384-aa Serratia plymuthica 4Rx13 SodD sequence (EMBL CP006250.1 protein AGO55049.1, locus tag SOD_c20750) and records that UniProtKB/TrEMBL entries S0AGG1.1, A0A318P116.1, and D1RQI7.1 are inactive/obsolete, confirming no active UniProtKB accession resolves for AGO55049.1.
SodD	forms	sodorifen	DOI:10.1021/jacs.8b08510 DOI:10.1093/femsle/fnw139 https://mibig.secondarymetabolites.org/repository/BGC0001361.3/BGC0001361.gbk https://www.ncbi.nlm.nih.gov/protein/AGO55049.1 https://www.uniprot.org/uniparc/UPI0001BED04F reference DOI:10.1021/jacs.8b08510 evidence type PRIMARY_EXPERIMENT snippet Methylation and Cyclization of MEP-Derived Farnesyl Pyrophosphate notes von Reuss et al. reconstituted Serratia plymuthica 4Rx13 SodD in vitro and placed the terpene cyclase downstream of SodC in the conversion of pre-sodorifen diphosphate to sodorifen. reference DOI:10.1093/femsle/fnw139 evidence type PRIMARY_EXPERIMENT notes Domik et al. assigned SOD_c20750 to the four-gene sodorifen biosynthetic cluster and used knockouts in Serratia plymuthica 4Rx13 to support its role in sodorifen production. reference https://mibig.secondarymetabolites.org/repository/BGC0001361.3/BGC0001361.gbk evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes MIBiG BGC0001361.3 places the Serratia plymuthica 4Rx13 SOD_c20750 CDS at complement(10001..11155) in the BGC GenBank row with protein_id AGO55049.1. reference https://www.ncbi.nlm.nih.gov/protein/AGO55049.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes NCBI GenPept AGO55049.1 is the Serratia plymuthica 4Rx13 SOD_c20750 sequence assigned here to SodD; no UniProtKB entry resolved for this accession or locus. reference https://www.uniprot.org/uniparc/UPI0001BED04F evidence type DATABASE_ASSERTION retrieved on 2026-10-23 snippet AGO55049.1 notes UniParc UPI0001BED04F archives the exact 384-aa Serratia plymuthica 4Rx13 SodD sequence (EMBL CP006250.1 protein AGO55049.1, locus tag SOD_c20750) and records that UniProtKB/TrEMBL entries S0AGG1.1, A0A318P116.1, and D1RQI7.1 are inactive/obsolete, confirming no active UniProtKB accession resolves for AGO55049.1.

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

Explore across X-Mech

AntibioticMech (sodorifen) ↗ MediaIngredientMech (naturalproductmech:mibig-0ea28266f1) ↗ TaxonMech: Serratia plymuthica 4Rx13 (NCBITaxon:682634) ↗ TaxonMech: Serratia plymuthica (NCBITaxon:82996) ↗ PathwayMech (mibig:BGC0001361) ↗ PathwayMech (mibig:BGC0002283) ↗

Open questions 1

shared-structure — This structure is reported by more than one MIBiG entry: BGC0001361, BGC0002283. Confirm they describe the same compound rather than an upstream cross-reference error.

Provenance

Source concept	Source	Version
BGC0001361	MIBIG	3
BGC0002283	MIBIG	2

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