agrochelin

CHEBI:65375 EXACT REVIEWED 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 member of the class thiazolidines that is (3S)-3-hydroxy-2,2-dimethyl-3-[(4R)-3-methyl-1,3-thiazolidin-4-yl]propanoic acid which is substituted at position 2 by a (4R)-2-(2-hydroxy-6-pentylphenyl)-4,5-dihydro-1,3-thiazol-4-yl group. A cytotoxic antibiotic, it is produced by the fermentation of Agrobacterium.

Structure

Standard InChIKey	QZBCDLLHQSDFIG-ZEVBXJOLSA-N
SMILES	[H][C@@]1([C@@H](O)C(C)(C)C(=O)O)CS[C@@]([H])([C@@]2([H])CSC(c3c(O)cccc3CCCCC)=N2)N1C
Stereochemistry	fully defined

Filing pathway

Unclassified — computed by NPClassifier npclassifier.gnps2.org@2026-10-31, which is why it is pinned rather than recomputed.

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
Agrobacterium sp. Strain: L-335-5 NCBITaxon:361	AXENIC_CULTURE		PMID:10656570 reference PMID:10656570 evidence type PRIMARY_EXPERIMENT notes Bioassay-guided isolation, 2D-NMR structure elucidation, and iron-chelation characterization of the thiazoline-thiazolidine alkaloid siderophore agrochelin from marine Agrobacterium sp. strain L-335-5.

Occurrences 1

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
Agrobacterium sp. NCBITaxon:361	CHEBI	PMID:10656570

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	Agrochelin hybrid PKS-NRPS synthetase		CHEBI:15351 + CHEBI:15531 + CHEBI:17561 → CHEBI:65375	PMID:10656570

Step 1: Hybrid PKS-NRPS assembly of a polyketide-derived 6-pentylsalicylate starter unit condensed with two L-cysteine residues (cyclized to tandem 4,5-dihydro-1,3-thiazole and N-methyl-1,3-thiazolidine rings) and a terminal 3-hydroxy-2,2-dimethylpropanoate unit in marine Agrobacterium sp. L-335-5 to yield agrochelin.

Mechanism & Biosynthesis Overview

Causal graph — bioactivity 7 nodes, 6 edges

Hybrid PKS-NRPS biosynthesis of the marine bacterial 6-pentylsalicyl-thiazoline-thiazolidine siderophore agrochelin in Agrobacterium sp. L-335-5, chelation of Fe(III), and iron-chelation-associated cytotoxicity.

Subject	Predicate	Object	Notes	Evidence
acetyl-CoA	substrate_of	Agrochelin hybrid PKS-NRPS synthetase	Starter unit for polyketide assembly of the 2-hydroxy-6-pentylphenyl moiety.	PMID:10656570 reference PMID:10656570 evidence type PRIMARY_EXPERIMENT notes Agrochelin contains a 2-hydroxy-6-pentylphenyl aromatic cap.
malonyl-CoA	substrate_of	Agrochelin hybrid PKS-NRPS synthetase	Extender units for the 6-pentylsalicylate and 3-hydroxy-2,2-dimethylpropanoate moieties.	PMID:31293678 reference PMID:31293678 evidence type PRIMARY_EXPERIMENT notes PKS modules assemble the 6-pentylsalicylate starter and dimethylmalonyl-derived C-terminal extension.
L-cysteine	substrate_of	Agrochelin hybrid PKS-NRPS synthetase	Two L-cysteine units are cyclized into the tandem 4,5-dihydro-1,3-thiazole and 3-methyl-1,3-thiazolidine rings.	PMID:10656570 reference PMID:10656570 evidence type PRIMARY_EXPERIMENT notes 2D-NMR structure elucidation identifies tandem dihydrothiazole and N-methylthiazolidine rings.
Agrochelin hybrid PKS-NRPS synthetase	synthesizes	agrochelin	Produces agrochelin in Agrobacterium sp. L-335-5.	PMID:10656570 reference PMID:10656570 evidence type PRIMARY_EXPERIMENT notes Isolation of agrochelin from marine Agrobacterium sp. L-335-5.
agrochelin	chelates	iron(3+)	Coordinates ferric iron(3+) via phenolate, thiazoline, thiazolidine, and beta-hydroxy acid donors.	PMID:10656570 reference PMID:10656570 evidence type PRIMARY_EXPERIMENT notes Siderophore iron-binding activity of agrochelin.
agrochelin	inhibits	cell population proliferation	Exhibits potent cytotoxicity against tumor cell lines via metal chelation.	PMID:10656570 reference PMID:10656570 evidence type PRIMARY_EXPERIMENT notes Sub-micromolar cytotoxicity of agrochelin against P388, A549, HT29, and MEL28 tumor cells.

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

Molecular targets 1

Target	Target organism	Measurement	Evidence
iron(3+) OTHER BINDS Chelation of ferric iron(3+) via the 2-(2-hydroxy-6-pentylphenyl)-4,5-dihydro-1,3-thiazol-4-yl (phenolate and thiazoline N), 3-methyl-1,3-thiazolidin-4-yl, and 3-hydroxy-2,2-dimethylpropanoate oxygen and nitrogen donor groups of agrochelin.			PMID:10656570 PMID:31293678 reference PMID:10656570 evidence type PRIMARY_EXPERIMENT notes Isolation, structural elucidation, and iron-chelating / cytotoxic characterization of the thiazoline-thiazolidine alkaloid siderophore agrochelin from the marine bacterium Agrobacterium sp. L-335-5. reference PMID:31293678 evidence type PRIMARY_EXPERIMENT notes Genomics-guided discovery and siderophore characterization of the agrochelin stereoisomer massiliachelin.

Elsewhere in the fleet

AntibioticMech — CHEBI:65375 (same structure, same inchikey)

Explore across X-Mech

AntibioticMech (agrochelin) ↗ MediaIngredientMech (CHEBI:65375) ↗ TaxonMech: Agrobacterium sp. (NCBITaxon:361) ↗

Provenance

Source concept	Source	Version
CHEBI:65375	CHEBI	3-star

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