NaturalProductMech

soraphen A

CHEBI:9200 EXACT SEEDED enzyme inhibitor

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 macrolide and an agent highly effective against plant-pathogenic fungi. It was extensively researched for agricultural use until it was discovered to be a teratogen.

Structure

Standard InChIKey	WPMGNXPRKGXGBO-OFQQMTDKSA-N
SMILES	C[C@H]1/C=C/[C@H]([C@H](CCCC[C@H](OC(=O)[C@H]([C@@]2([C@@H]([C@H]([C@@H]([C@H]1O2)C)O)OC)O)C)C3=CC=CC=C3)OC)OC
Stereochemistry	fully defined
Cross-references	pubchem:5281897

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.

Taxon	Basis	Cluster	Evidence
Sorangium cellulosum NCBITaxon:56	SOURCE_ASSERTION	mibig:BGC0000147	PMID:12039053

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.

Taxon	Source	Reference
Sorangium cellulosum So ce56 NCBITaxon:448385	CHEBI	PMID:7916271
Sorangium cellulosum NCBITaxon:56	LOTUS	DOI:10.1002/JLAC.1993199301161
Sorangium cellulosum NCBITaxon:56	LOTUS	DOI:10.1016/S0378-1119(02)00396-7
Sorangium cellulosum NCBITaxon:56	LOTUS	DOI:10.1016/S1389-1723(04)70202-9
Sorangium cellulosum NCBITaxon:56	LOTUS	DOI:10.1039/A806112B
Sorangium cellulosum NCBITaxon:56	LOTUS	DOI:10.7164/ANTIBIOTICS.47.23

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000147	Sorangium cellulosum NCBITaxon:56	CLUSTER_DEMONSTRATED	genbank:U24241.2

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.

Mechanism & Biosynthesis Overview

Causal graph — bioactivity 2 nodes, 1 edge

Soraphen A binds the human acetyl-CoA carboxylase 2 biotin carboxylase domain captured in PDB 3JRX.

Subject	Predicate	Object	Notes	Evidence
soraphen A	binds	human acetyl-CoA carboxylase 2	PubChem BioAssay AID 977611 maps this exact Standard InChIKey to an active 0.001 uM Kd row for PDB 3JRX chain A; PDBe maps 3JRX_A to the Homo sapiens UniProtKB:O00763 ACC2 sequence, and RCSB reports S1A soraphen A with the record's Standard InChIKey as a 3JRX non-polymer ligand. Chain A is a biotin carboxylase domain construct spanning ACC2 residues 217-775 with affinity tags.	DOI:10.1016/j.bbrc.2009.11.029 DOI:10.2210/pdb3jrx/pdb reference DOI:10.1016/j.bbrc.2009.11.029 evidence type PRIMARY_EXPERIMENT snippet We also determined the structure of the human BC domain in complex with soraphen A notes Cho et al. solved PDB 3JRX as a human ACC2 biotin carboxylase domain structure with bound soraphen A. reference DOI:10.2210/pdb3jrx/pdb evidence type DATABASE_ASSERTION notes RCSB PDB identifies 3JRX as a human ACC2 biotin carboxylase domain crystal structure containing S1A soraphen A, and PDBe maps chain A to Homo sapiens UniProtKB:O00763.

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

Causal graph — bioactivity 2 nodes, 1 edge

Soraphen A binds the Saccharomyces cerevisiae acetyl-CoA carboxylase biotin carboxylase domain captured in PDB 1W96.

Subject	Predicate	Object	Notes	Evidence
soraphen A	binds	Saccharomyces cerevisiae acetyl-CoA carboxylase Acc1	PubChem BioAssay AID 977611 maps this exact Standard InChIKey to an active 0.0039 uM Kd row for PDB 1W96 chain A; PDBe maps 1W96 chains A, B, and C to Saccharomyces cerevisiae UniProtKB:Q00955 residues 13-566, and RCSB reports S1A soraphen A with the record's Standard InChIKey as a 1W96 non-polymer ligand.	DOI:10.1016/J.MOLCEL.2004.11.034 DOI:10.2210/pdb1w96/pdb reference DOI:10.1016/J.MOLCEL.2004.11.034 evidence type PRIMARY_EXPERIMENT snippet A Mechanism for the Potent Inhibition of Eukaryotic Acetyl-Coenzyme a Carboxylase by Soraphen A, a Macrocyclic Polyketide Natural Product notes Shen et al. solved the S. cerevisiae ACC1 biotin carboxylase domain structure with bound soraphen A, deposited as PDB 1W96. reference DOI:10.2210/pdb1w96/pdb evidence type DATABASE_ASSERTION snippet Crystal Structure of Biotin Carboxylase Domain of Acetyl-coenzyme A Carboxylase from Saccharomyces cerevisiae in Complex with Soraphen A notes RCSB PDB identifies 1W96 as a Saccharomyces cerevisiae acetyl-CoA carboxylase biotin carboxylase domain crystal structure containing S1A soraphen A, and PDBe maps its protein chains to UniProtKB:Q00955.

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

Causal graph — biosynthesis 2 nodes, 1 edge

Native-reference identity for Sorangium cellulosum So ce26, taxon 56/U24241.2/BGC0000147. So ce26 is not equated with the record's separate So ce56 occurrence. Matching references do not establish measured expression, a verified assay construct, enzyme activity, native assembly, modification or cofactor occupancy.

Subject	Predicate	Object	Notes	Evidence
sorM CDS (U24241.2)	encodes the native protein reference	SorM (So ce26 native-reference example)	Forward-strand 60255..61295; 1041-nt complete CDS including stop, 346 residues.	https://www.ncbi.nlm.nih.gov/nuccore/U24241.2 https://www.ncbi.nlm.nih.gov/protein/AAK19894.1 https://www.uniprot.org/uniprotkb/Q9ADL4/entry https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000318.json reference https://www.ncbi.nlm.nih.gov/nuccore/U24241.2 evidence type DATABASE_ASSERTION notes GenBank names sorM and assigns AAK19894.1, codon_start 1, translation table 11. The complete 67,523-bp U24241.2 reference identifies So ce26/taxon 56; this is a deposited sequence annotation, not an enzyme assay. retrieved on 2026-10-08 snippet /gene="sorM" reference https://www.ncbi.nlm.nih.gov/protein/AAK19894.1 evidence type DATABASE_ASSERTION notes GenPept identifies So ce26/taxon 56 and conceptual translation. Its coded_by points to the same U24241.2 CDS coordinates. retrieved on 2026-10-08 reference https://www.uniprot.org/uniprotkb/Q9ADL4/entry evidence type CURATOR_INFERENCE notes Unreviewed entry version 52, sequence version 1, with So ce26 strain references. CDS-aware translation, deposited translation, GenPept and UniProt agree over all 346 residues. No specific FUNCTION or CATALYTIC ACTIVITY comment. Computational family, function, PTM and cofactor annotations are not direct enzyme evidence. Predicted sterol C-methyltransferase GO annotations do not establish native substrate specificity. retrieved on 2026-10-08 reference https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000318.json evidence type DATABASE_ASSERTION notes Active MITE0000318 version 1 maps SorM to Q9ADL4/AAK19894.1/BGC0000147. Native sequence identity does not independently validate the reaction annotation. retrieved on 2026-10-08

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

Causal graph — biosynthesis 2 nodes, 1 edge

Native-reference identity for Sorangium cellulosum So ce26, taxon 56/U24241.2/BGC0000147. So ce26 is not equated with the record's separate So ce56 occurrence. Matching references do not establish measured expression, a verified assay construct, enzyme activity, native assembly, modification or cofactor occupancy.

Subject	Predicate	Object	Notes	Evidence
sorR CDS (U24241.2)	encodes the native protein reference	SorR (So ce26 native-reference example)	Forward-strand 13697..14158; 462-nt complete CDS including stop, 153 residues.	https://www.ncbi.nlm.nih.gov/nuccore/U24241.2 https://www.ncbi.nlm.nih.gov/protein/AAK19893.1 https://www.uniprot.org/uniprotkb/Q9ADL7/entry https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000468.json reference https://www.ncbi.nlm.nih.gov/nuccore/U24241.2 evidence type DATABASE_ASSERTION notes GenBank names sorR and assigns AAK19893.1, codon_start 1, translation table 11. The complete 67,523-bp U24241.2 reference identifies So ce26/taxon 56; this is a deposited sequence annotation, not an enzyme assay. retrieved on 2026-10-08 snippet /gene="sorR" reference https://www.ncbi.nlm.nih.gov/protein/AAK19893.1 evidence type DATABASE_ASSERTION notes GenPept identifies So ce26/taxon 56 and conceptual translation. Its coded_by points to the same U24241.2 CDS coordinates. retrieved on 2026-10-08 reference https://www.uniprot.org/uniprotkb/Q9ADL7/entry evidence type CURATOR_INFERENCE notes Unreviewed entry version 64, sequence version 1, with So ce26 strain references. CDS-aware translation, deposited translation, GenPept and UniProt agree over all 153 residues. No specific FUNCTION or CATALYTIC ACTIVITY comment. Computational family, function, PTM and cofactor annotations are not direct enzyme evidence. Predicted fatty-acid synthase GO and phosphopantetheine/phosphoprotein keywords are not verified activities or modifications. The MITE0000468 reaction is withheld under https://github.com/CultureBotAI/NaturalProductMech/issues/697: its Reduction tag, possible oxidation/hemiacetalization description and modeled C28H46O9 to C28H44O8 need reconciliation. No catalytic reaction edge or measured NADP specificity is added. retrieved on 2026-10-08 reference https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000468.json evidence type DATABASE_ASSERTION notes Active MITE0000468 version 1 maps SorR to Q9ADL7/AAK19893.1/BGC0000147. Native sequence identity does not independently validate the reaction annotation. retrieved on 2026-10-08

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

Causal graph — biosynthesis 4 nodes, 3 edges

Partial inferred O-methylation model from MITE0000318 version 1. MITE labels its evidence Inference from genomic data and chemical structure and cites DOI:10.1016/S0378-1119(02)00396-7. Only the search-returned paper abstract was inspected; a subsequent official PubMed open returned 429 and retrieval stopped. No primary full-text enzyme assay is adopted. The database names soraphen C to soraphen A, but its product omits alkene geometry, so no exact owner-product identity is asserted. This is not an ordered or complete pathway; chemical/process nodes remain ungrounded.

Subject	Predicate	Object	Notes	Evidence
SorM (So ce26 native-reference example)	is inferred by the database to catalyze	proposed O-methylation (inferred model)	Genomic/chemical inference, not a directly inspected enzyme experiment.	https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000318.json reference https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000318.json evidence type DATABASE_ASSERTION notes Active MITE0000318 version 1 proposes post-PKS C11 O-methylation. No rates, measured cofactor specificity, assembly or verified native-substrate assay are adopted. retrieved on 2026-10-08 snippet Responsible for the post-PKS O-methylation of the hydroxyl at C11
SorM substrate (MITE model)	is the modeled substrate of	proposed O-methylation (inferred model)	Source model only; no independently verified assay substrate or reaction order.	https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000318.json reference https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000318.json evidence type DATABASE_ASSERTION notes RDKit 2026.03.5 substrate key USIRVOOCIGRCRU-CXBYLNABSA-N, C28H42O8. Different connectivity from the owner; no ChEBI/Rhea identifier chosen. retrieved on 2026-10-08
proposed O-methylation (inferred model)	is modeled to yield	SorM product (MITE model)	Inferred model, not exact stereochemically specified soraphen A.	https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000318.json reference https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000318.json evidence type DATABASE_ASSERTION notes RDKit 2026.03.5 product key WPMGNXPRKGXGBO-JXOLNOSBSA-N, C29H44O8. It shares owner connectivity but not the exact key; ten tetrahedral centers are specified and one double bond is unspecified. Missing geometry is not filled from substrate or owner. MITE marks this example as an intermediate; no automatic inter-graph bridge is made. retrieved on 2026-10-08

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

Bioactivities 4

Entries preserve source qualifiers, targets and evidence. Repeated assay names or values are not independent replications; inspect source detail for differences.

Assay	Result	Target enzyme	Source detail
ACCase Enzymatic Assay from US Patent US11375716: "Acetyl-CoA carboxylase modulators"	IC50 0.0458 uM; ACTIVE	UniProtKB:A0A0D1DYD5	pubchem.aid:1806637 assay ACCase Enzymatic Assay from US Patent US11375716: "Acetyl-CoA carboxylase modulators" evidence reference pubchem.aid:1806637 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1806637, deposited by BindingDB; assay type Confirmatory. call ACTIVE measurement type IC50 value 0.0458 units uM target enzyme UniProtKB:A0A0D1DYD5
Experimentally measured binding affinity data (Kd) for protein-ligand complexes derived from PDB	KD 0.0039 uM; ACTIVE	Not recorded	pubchem.aid:977611 assay Experimentally measured binding affinity data (Kd) for protein-ligand complexes derived from PDB evidence reference pubchem.aid:977611 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 977611, deposited by Shanghai Institute of Organic Chemistry; assay type Other. Target accession 1W96_A was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type KD value 0.0039 units uM activity class ENZYME_INHIBITOR
Experimentally measured binding affinity data (Kd) for protein-ligand complexes derived from PDB	KD 0.001 uM; ACTIVE	Not recorded	PMID:19900410 assay Experimentally measured binding affinity data (Kd) for protein-ligand complexes derived from PDB evidence reference PMID:19900410 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 977611, deposited by Shanghai Institute of Organic Chemistry; assay type Other. Target accession 3JRX_A was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type KD value 0.001 units uM activity class ENZYME_INHIBITOR
Experimentally measured binding affinity data derived from PDB	ACTIVE	Not recorded	pubchem.aid:1811 assay Experimentally measured binding affinity data derived from PDB evidence reference pubchem.aid:1811 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1811, deposited by Shanghai Institute of Organic Chemistry; assay type Other. Target accession 1W96_A was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE activity class ENZYME_INHIBITOR

Explore across X-Mech

AntibioticMech (soraphen A) ↗ MediaIngredientMech (CHEBI:9200) ↗ TaxonMech: Sorangium cellulosum (NCBITaxon:56) ↗ PathwayMech (mibig:BGC0000147) ↗

Provenance

Source concept	Source	Version
BGC0000147	MIBIG	5
CHEBI:9200	CHEBI	3-star

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