chondrochloren A

CHEBI:132426 EXACT SEEDED antimicrobial unspecified

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 monocarboxylic acid amide with formula C27H40ClNO7, that is produced by Chondromyces crocatus and exhibits antibiotic properties.

Structure

Standard InChIKey	FYBGSKAWXCBCIQ-JRAUAZSASA-N
SMILES	CCCC[C@@H](C)[C@H](O)[C@H](C)C(=O)C(\C)=C\[C@@H](OC)[C@@H](O)[C@@H](OC)C(=O)N\C=C/C1=CC=C(O)C(Cl)=C1
Stereochemistry	fully defined
Cross-references	npatlas:NPA0508

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 nrps, 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
Chondromyces crocatus NCBITaxon:52	BGC_CHARACTERIZED	mibig:BGC0000970	PMID:19171307

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
Chondromyces crocatus NCBITaxon:52	LOTUS	DOI:10.1002/EJOC.200200699
Chondromyces crocatus NCBITaxon:52	CHEBI	PMID:19171307

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000970	Chondromyces crocatus NCBITaxon:52	CLUSTER_DEMONSTRATED	genbank:AM988861.1

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	CndG 1'-carboxy-chondrochloren decarboxylase UniProtKB:B9ZUK6	RHEA:81491	CHEBI:231889 + CHEBI:57692 → CHEBI:132426	DOI:10.1074/jbc.M109.079707

Step 1: CndG carries out the terminal FAD-dependent oxidative decarboxylation of 1'-carboxy-chondrochloren A to form mature chondrochloren A; Rhea maps the corresponding EC 4.1.1.129 reaction to RHEA:81491.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 3 nodes, 2 edges

Partial C. crocatus chondrochloren A biosynthesis graph for CndG-catalyzed terminal oxidative decarboxylation.

Subject	Predicate	Object	Notes	Evidence
1'-carboxy-chondrochloren A	is oxidatively decarboxylated by	CndG 1'-carboxy-chondrochloren decarboxylase	CndG oxidatively decarboxylates the carboxylated pre-chondrochloren A precursor.	DOI:10.1074/jbc.M109.079707 DOI:10.1016/j.chembiol.2008.11.005 https://mibig.secondarymetabolites.org/repository/BGC0000970.5/BGC0000970.gbk https://www.uniprot.org/uniprotkb/B9ZUK6 https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv reference DOI:10.1074/jbc.M109.079707 evidence type PRIMARY_EXPERIMENT snippet shown to be an FAD-dependent oxidative decarboxylase notes Rachid et al. inactivated cndG in Chondromyces crocatus Cm c5, observed pre-chondrochloren accumulation and loss of mature chondrochloren production, then expressed CndG in E. coli and assayed oxidative decarboxylation of pre-chondrochlorens. reference DOI:10.1016/j.chembiol.2008.11.005 evidence type PRIMARY_EXPERIMENT notes Rachid et al. sequenced the AM988861 chondrochloren biosynthetic gene cluster from C. crocatus Cm c5 and nominated CndG as the candidate oxidative decarboxylase. reference https://mibig.secondarymetabolites.org/repository/BGC0000970.5/BGC0000970.gbk evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes MIBiG BGC0000970.5 maps the C. crocatus AM988861 chondrochloren biosynthetic gene cluster CDS CAQ43085.1 to cndG and cross-references UniProtKB:B9ZUK6. reference https://www.uniprot.org/uniprotkb/B9ZUK6 evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes Reviewed UniProtKB:B9ZUK6 is the 541 aa C. crocatus CndG 1'-carboxy-chondrochloren decarboxylase, cross-references AM988861 protein CAQ43085.1, and annotates RHEA:81491 from PMID:20080978. reference https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes The Rhea Swiss-Prot mapping links UniProtKB:B9ZUK6 to RHEA:81491, the EC 4.1.1.129 1'-carboxy-chondrochloren A decarboxylation reaction.
CndG 1'-carboxy-chondrochloren decarboxylase	forms	chondrochloren A	The CndG reaction yields mature chondrochloren A from the inactive carboxylated precursor.	DOI:10.1074/jbc.M109.079707 DOI:10.1016/j.chembiol.2008.11.005 https://mibig.secondarymetabolites.org/repository/BGC0000970.5/BGC0000970.gbk https://www.uniprot.org/uniprotkb/B9ZUK6 https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv reference DOI:10.1074/jbc.M109.079707 evidence type PRIMARY_EXPERIMENT snippet shown to be an FAD-dependent oxidative decarboxylase notes Rachid et al. inactivated cndG in Chondromyces crocatus Cm c5, observed pre-chondrochloren accumulation and loss of mature chondrochloren production, then expressed CndG in E. coli and assayed oxidative decarboxylation of pre-chondrochlorens. reference DOI:10.1016/j.chembiol.2008.11.005 evidence type PRIMARY_EXPERIMENT notes Rachid et al. sequenced the AM988861 chondrochloren biosynthetic gene cluster from C. crocatus Cm c5 and nominated CndG as the candidate oxidative decarboxylase. reference https://mibig.secondarymetabolites.org/repository/BGC0000970.5/BGC0000970.gbk evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes MIBiG BGC0000970.5 maps the C. crocatus AM988861 chondrochloren biosynthetic gene cluster CDS CAQ43085.1 to cndG and cross-references UniProtKB:B9ZUK6. reference https://www.uniprot.org/uniprotkb/B9ZUK6 evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes Reviewed UniProtKB:B9ZUK6 is the 541 aa C. crocatus CndG 1'-carboxy-chondrochloren decarboxylase, cross-references AM988861 protein CAQ43085.1, and annotates RHEA:81491 from PMID:20080978. reference https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes The Rhea Swiss-Prot mapping links UniProtKB:B9ZUK6 to RHEA:81491, the EC 4.1.1.129 1'-carboxy-chondrochloren A decarboxylation reaction.

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 only for CndH in Chondromyces crocatus Cm c5/taxon 52/AM988861.1. Placement in this owner is curator-inferred from the shared BGC0000970 context, not proof of an exact-product reaction. The MITE wildcard phenol model does not identify a complete carrier-bound substrate; carrier and reductase are not assigned. No chlorination, deletion phenotype, pathway order or physical complex is asserted. Historical UniProtKB:B9ZUJ5 is deleted; its UniParc identifier is not a current UniProtKB example. The CndH primary paper (DOI:10.1016/j.jmb.2008.10.057) returned HTTP 403 and the distinct cluster paper (DOI:10.1016/j.chembiol.2008.11.005) was inaccessible on 2026-10-08; retrieval stopped for both. No primary CndH experiment is independently adopted.

Subject	Predicate	Object	Notes	Evidence
cndH CDS (AM988861.1)	encodes the native protein reference	CndH (C. crocatus Cm c5 native-reference example)	5294..6832 reverse strand; 1539-nt complete CDS including stop, 512 residues. The deposited PDB sample sequence matches, but this does not establish all coordinate residues, tag processing, the full experimental preparation or activity. Native sequence identity is distinct from a primary reaction claim.	https://www.ncbi.nlm.nih.gov/nuccore/AM988861.1 https://www.ncbi.nlm.nih.gov/protein/CAQ43074.1 https://data.rcsb.org/rest/v1/core/polymer_entity/3E1T/1 https://rest.uniprot.org/uniprotkb/B9ZUJ5.json https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000494.json https://www.ncbi.nlm.nih.gov/nuccore/AM988861.1 reference https://www.ncbi.nlm.nih.gov/nuccore/AM988861.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-08 snippet /gene="cndH" notes The 51,243-bp cluster deposition annotates cndH/CAQ43074.1 at complement(5294..6832), codon_start 1, translation table 11, strain Cm c5/taxon 52. The deposited halogenase label is not independently inspected activity evidence. reference https://www.ncbi.nlm.nih.gov/protein/CAQ43074.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-08 notes Versioned GenPept CAQ43074.1 is the 512-residue C. crocatus Cm c5 conceptual translation of cndH and explicitly codes from complement(AM988861.1:5294..6832). Its historical B9ZUJ5 cross-reference must not be treated as an active UniProtKB entry. reference https://data.rcsb.org/rest/v1/core/polymer_entity/3E1T/1 evidence type DATABASE_ASSERTION retrieved on 2026-10-08 notes Independent PDB 3E1T entity 1 deposition (chain A) gives a 512-residue sample sequence, cndh source gene and C. crocatus taxon 52. It names E. coli as expression host, not as native producer. This is deposited sequence metadata, not a read of the inaccessible paper methods or proof that every residue is resolved. reference https://rest.uniprot.org/uniprotkb/B9ZUJ5.json evidence type DATABASE_ASSERTION retrieved on 2026-10-08 snippet Not part of a reference proteome notes Current endpoint reports entryType Inactive and inactiveReasonType DELETED, linking historical B9ZUJ5 to UniParc UPI0001932834. Neither is selected as a current UniProtKB example. Deletion is not evidence that the native protein does not exist. reference https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000494.json evidence type DATABASE_ASSERTION retrieved on 2026-10-08 notes Pinned active MITE0000494 v1 links CndH with CAQ43074.1 and BGC0000970. Its uniprot field contains a UniParc identifier. Its wildcard phenol chlorination model and heterologous-expression evidence code are not promoted into an independently verified complete-substrate reaction. reference https://www.ncbi.nlm.nih.gov/nuccore/AM988861.1 evidence type CURATOR_INFERENCE retrieved on 2026-10-08 notes Complete-CDS-aware reverse-strand translation, deposited translation, separate GenPept and PDB entity 1 sample sequence agree over all 512 residues. Matching gene, accession, native strain and taxon establish this reference identity. Placement in this owner is inferred from its existing AM988861.1/BGC0000970 context, not from an experiment on the exact owner. The current exact-gene/taxon or accession UniProtKB query returned zero entries; this bounded result does not establish global database absence.

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

Elsewhere in the fleet

AntibioticMech — CHEBI:132426 (same structure, same inchikey)

Explore across X-Mech

AntibioticMech (chondrochloren A) ↗ MediaIngredientMech (CHEBI:132426) ↗ TaxonMech: Chondromyces crocatus (NCBITaxon:52) ↗ PathwayMech (mibig:BGC0000970) ↗

Provenance

Source concept	Source	Version
BGC0000970	MIBIG	5
CHEBI:132426	CHEBI	3-star

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