formobactin

CHEBI:65906 EXACT REVIEWED antimicrobial unspecified

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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

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A cyclic hydroxamic acid derivative and antibiotic isolated from Nocardia sp. strain ND20. It exerts an inhibitory effect on lipid peroxidation and also has a potent protecting effect on neuronal cells.

Structure

Standard InChIKey	ZZBSPTCNZDTZBR-QGXZNONUSA-N
SMILES	CCCCCCCCCC(OC(=O)[C@H](CCCCN(O)C=O)NC(=O)c1nc(-c2ccccc2O)oc1C)C(C)(C)C(=O)NC1CCCCN(O)C1=O
Stereochemistry	undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers

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
Nocardia Strain: ND20 NCBITaxon:1821	AXENIC_CULTURE		PMID:8931715 reference PMID:8931715 evidence type PRIMARY_EXPERIMENT notes Isolation, NMR/MS structure elucidation, and free-radical scavenging characterization of the nocobactin-like phenyloxazole-hydroxamate-formylhydroxamate siderophore formobactin from Nocardia sp. strain ND20.

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
Nocardia NCBITaxon:1821	CHEBI	PMID:8931715

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	Formobactin NRPS-PKS synthetase		CHEBI:16914 + CHEBI:15729 + CHEBI:79095 → CHEBI:65906	PMID:8931715

Step 1: Nonribosomal condensation of salicylic acid, L-threonine (cyclized to 5-methyl-1,3-oxazole), an N-formyl-N-hydroxy-L-ornithine / alkyl-malonyl-derived spacer, and a C-terminal N-hydroxy-L-ornithine cyclic hydroxamate in Nocardia sp. ND20 to yield formobactin.

Mechanism & Biosynthesis Overview

Causal graph — bioactivity 8 nodes, 7 edges

Biosynthesis of the phenyloxazole-hydroxamate siderophore formobactin in Nocardia sp. ND20, hexadentate chelation of Fe(III)/Fe(II), and inhibition of iron-dependent oxidative stress and lipid peroxidation.

Subject	Predicate	Object	Notes	Evidence
salicylic acid	substrate_of	Formobactin NRPS-PKS synthetase	Forms the 2-hydroxyphenyl-5-methyloxazole chelating cap.	PMID:8931715 reference PMID:8931715 evidence type PRIMARY_EXPERIMENT notes Formobactin contains a 2-(2-hydroxyphenyl)-5-methyloxazole-4-carboxamide cap.
L-ornithine	converted_to	N(5)-hydroxy-L-ornithine	N5-hydroxylation generates the hydroxamate building blocks.	PMID:8931715 reference PMID:8931715 evidence type PRIMARY_EXPERIMENT notes Formobactin contains N-formylhydroxamate and cyclic N-hydroxyornithine lactam moieties.
N(5)-hydroxy-L-ornithine	substrate_of	Formobactin NRPS-PKS synthetase	Incorporated into the internal N-formylhydroxamate and terminal cyclic hydroxamate rings.	PMID:8931715 reference PMID:8931715 evidence type PRIMARY_EXPERIMENT notes NMR structure elucidation of formobactin.
Formobactin NRPS-PKS synthetase	synthesizes	formobactin	Produces formobactin in Nocardia sp. ND20.	PMID:8931715 reference PMID:8931715 evidence type PRIMARY_EXPERIMENT notes Purification of formobactin from Nocardia sp. ND20 mycelium.
formobactin	chelates	iron(3+)	Hexadentate coordination of ferric iron(3+) via phenolate, oxazole N, and two hydroxamate groups.	PMID:8931715 reference PMID:8931715 evidence type PRIMARY_EXPERIMENT notes Iron-binding characterization of formobactin.
formobactin	chelates	iron(2+)	Sequesters catalytic iron to block Fenton-type lipid peroxidation (IC50 = 0.065 uM).	PMID:8931715 reference PMID:8931715 evidence type PRIMARY_EXPERIMENT notes Inhibition of lipid peroxidation in rat brain homogenate by formobactin.
formobactin	regulates	response to oxidative stress	Protects cells against iron-catalyzed free-radical oxidative damage.	PMID:8931715 reference PMID:8931715 evidence type PRIMARY_EXPERIMENT notes Suppression of free radical generation and glutamate-induced neurotoxicity.

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

Molecular targets 2

Target	Target organism	Measurement	Evidence
iron(3+) OTHER BINDS Hexadentate coordination of ferric iron(3+) via the 2-(2-hydroxyphenyl)-5-methyl-1,3-oxazole-4-carboxamide phenolate/oxazoline N,O-donors, the central N-formylhydroxamate group, and the terminal cyclic N-hydroxyornithine hydroxamate lactam in Nocardia sp. ND20.			PMID:8931715 reference PMID:8931715 evidence type PRIMARY_EXPERIMENT notes Isolation, structural elucidation, and iron-chelating / radical-scavenging characterization of formobactin from Nocardia sp. ND20.
iron(2+) OTHER BINDS Suppression of iron-catalyzed lipid peroxidation in rat brain homogenate (IC50 = 0.065 uM) by chelating iron cations and preventing Fenton radical generation.			PMID:8931715 reference PMID:8931715 evidence type PRIMARY_EXPERIMENT notes Formobactin potently inhibits iron-induced lipid peroxidation in rat brain homogenate (IC50 = 0.065 uM) and protects neural cells from L-glutamate toxicity.

Elsewhere in the fleet

AntibioticMech — CHEBI:65906 (same structure, same inchikey)

Explore across X-Mech

AntibioticMech (formobactin) ↗ MediaIngredientMech (CHEBI:65906) ↗ TaxonMech: Nocardia (NCBITaxon:1821) ↗

Provenance

Source concept	Source	Version
CHEBI:65906	CHEBI	3-star

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