desferrioxamine D1

CHEBI:50456 EXACT REVIEWED

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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

An acyclic desferrioxamine that is the N-acetyl derivative of desferrioxamine B.

Structure

Standard InChIKey	IEYBTYRDMTXDKO-UHFFFAOYSA-N
SMILES	CC(=O)NCCCCCN(O)C(=O)CCC(=O)NCCCCCN(O)C(=O)CCC(=O)NCCCCCN(O)C(C)=O
Stereochemistry	fully defined

Filing pathway

Fatty acids — computed by NPClassifier npclassifier.gnps2.org@2026-10-30, which is why it is pinned rather than recomputed. The gene cluster's asserted class is other, 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
Streptomyces coelicolor A3(2) Strain: M145 NCBITaxon:100226	BGC_CHARACTERIZED	mibig:BGC0000940	PMID:15600304 reference PMID:15600304 evidence type PRIMARY_EXPERIMENT notes Biosynthesis of the N-acetylated linear trihydroxamate siderophore desferrioxamine D1 by Streptomyces coelicolor M145 is directed by the genetically characterized desABCD locus (mibig:BGC0000940).
Streptomyces coelicolor A3(2) Strain: A3(2) NCBITaxon:100226	BGC_CHARACTERIZED	mibig:BGC0000940	PMID:29685972 reference PMID:29685972 evidence type PRIMARY_EXPERIMENT notes Structural and biochemical characterization of the Streptomyces coelicolor A3(2) acyltransferase DesC (mibig:BGC0000940) demonstrates substrate-tolerant acylation of N-hydroxycadaverine with acetyl-CoA and succinyl-CoA during assembly of acetylated linear desferrioxamines including desferrioxamine D1.

Occurrences 0

None cited.

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000940	Streptomyces coelicolor A3(2) NCBITaxon:100226	CLUSTER_DEMONSTRATED	genbank:AL645882.2

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.

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	DesA (lysine decarboxylase) and DesB (cadaverine monooxygenase)		CHEBI:18019 → CHEBI:18127	PMID:15600304
2	DesC (acyltransferase) and DesD (NIS siderophore synthetase)		CHEBI:18127 + CHEBI:15351 + CHEBI:15380 → CHEBI:50456	PMID:29685972

Step 1: Decarboxylation of L-lysine to cadaverine and FAD-dependent N-hydroxylation to N-hydroxycadaverine in the Streptomyces desABCD pathway.

Step 2: Acylation of N-hydroxycadaverine with acetyl-CoA and succinyl-CoA followed by ATP-dependent trimerization and terminal N-acetylation to yield desferrioxamine D1 (N-acetyl-desferrioxamine B).

Mechanism & Biosynthesis Overview

Causal graph — bioactivity 10 nodes, 9 edges

Biosynthesis of N-acetylated linear tris-hydroxamate siderophore desferrioxamine D1 via the desABCD cluster and chelation of Fe(III), CMM cations Ga(III), Co(II), Ni(II), and divalent transition metals Cu(II) and Zn(II).

Subject	Predicate	Object	Notes	Evidence
L-lysine	substrate_of	desABCD biosynthetic gene cluster (BGC0000940)	L-lysine is decarboxylated and N-hydroxylated by DesA and DesB.	PMID:15600304 reference PMID:15600304 evidence type PRIMARY_EXPERIMENT notes DesA and DesB convert L-lysine into N-hydroxycadaverine.
acetyl-CoA	substrate_of	desABCD biosynthetic gene cluster (BGC0000940)	Acetyl-CoA provides the terminal N-acetyl group and N-acetyl-N-hydroxycadaverine cap via DesC.	PMID:29685972 reference PMID:29685972 evidence type PRIMARY_EXPERIMENT notes DesC utilizes acetyl-CoA to form N-acetylated hydroxamate units.
succinyl-CoA	substrate_of	desABCD biosynthetic gene cluster (BGC0000940)	Succinyl-CoA provides internal succinyl spacers via DesC.	PMID:29685972 reference PMID:29685972 evidence type PRIMARY_EXPERIMENT notes DesC condenses N-hydroxycadaverine with succinyl-CoA.
desABCD biosynthetic gene cluster (BGC0000940)	synthesizes	desferrioxamine D1	Assembles N-acetyl-desferrioxamine B (desferrioxamine D1).	PMID:29685972 reference PMID:29685972 evidence type PRIMARY_EXPERIMENT notes Substrate-tolerant DesC and DesD assemble acetyl- and succinyl-containing desferrioxamines.
desferrioxamine D1	chelates	iron(3+)	Forms octahedral 1:1 ferrioxamine D1 complex.	PMID:24606332 reference PMID:24606332 evidence type PRIMARY_EXPERIMENT notes Octahedral ferric tris-hydroxamate coordination by linear ferrioxamine siderophores.
iron(3+)	enables	siderophore transport	Delivers ferric iron via bacterial ferrioxamine transport systems.	PMID:24606332 reference PMID:24606332 evidence type PRIMARY_EXPERIMENT notes Ferric-ferrioxamine complexes are recognized and imported by FhuD-family siderophore transporters.
desferrioxamine D1	chelates	gallium(3+)	[CMM] In vitro hexadentate coordination of gallium(3+).	PMID:25087170 reference PMID:25087170 evidence type PRIMARY_EXPERIMENT notes Hexadentate Ga(III) complexation by linear tris-hydroxamate desferrioxamines.
desferrioxamine D1	chelates	cobalt(2+)	[CMM] In vitro coordination of cobalt(2+).	PMID:22641620 reference PMID:22641620 evidence type PRIMARY_EXPERIMENT notes Divalent Co(II) chelation by linear tris-hydroxamate desferrioxamines.
desferrioxamine D1	chelates	nickel(2+)	[CMM] In vitro coordination of nickel(2+).	PMID:22641620 reference PMID:22641620 evidence type PRIMARY_EXPERIMENT notes Divalent Ni(II) chelation by linear tris-hydroxamate desferrioxamines.

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

Molecular targets 6

Target	Target organism	Measurement	Evidence
iron(3+) OTHER BINDS Primary physiological ferric ion chelation via hexadentate tris-hydroxamate coordination (ferrioxamine D1, N-acetyl-desferrioxamine B, 1:1 complex, log beta110 = 30.76) for bacterial iron acquisition.			PMID:29685972 PMID:24606332 reference PMID:29685972 evidence type PRIMARY_EXPERIMENT notes Substrate-tolerant acyltransferase DesC incorporates both acetyl-CoA and succinyl-CoA in Streptomyces desferrioxamine biosynthesis, generating N-acetylated linear tris-hydroxamate desferrioxamines. reference PMID:24606332 evidence type PRIMARY_EXPERIMENT notes Crystal and solution structural characterization of ferric tris-hydroxamate ferrioxamine recognition by bacterial siderophore-binding lipoprotein FhuD2.
gallium(3+) OTHER BINDS [Critical Mineral & Material (CMM)] Hexadentate tris-hydroxamate coordination of trivalent gallium(3+) (log beta110 ~ 27.8, measured in vitro in aqueous solution; slightly lower affinity than Fe(III)).			PMID:25087170 reference PMID:25087170 evidence type PRIMARY_EXPERIMENT notes Comparison of hexadentate tris-hydroxamate desferrioxamine complexation with Ga(III) and Fe(III) in aqueous solution.
cobalt(2+) OTHER BINDS [Critical Mineral & Material (CMM)] Coordination of divalent cobalt(2+) in aqueous solution (log beta110 ~ 10.3, measured in vitro only; >20 orders of magnitude weaker than Fe(III)).			PMID:22641620 reference PMID:22641620 evidence type PRIMARY_EXPERIMENT notes Characterization of linear tris-hydroxamate desferrioxamine complexation with divalent Co(II), Ni(II), Cu(II), and Zn(II) in aqueous solution.
nickel(2+) OTHER BINDS [Critical Mineral & Material (CMM)] Coordination of divalent nickel(2+) in aqueous solution (log beta110 ~ 10.9, measured in vitro only; non-physiological secondary binding).			PMID:22641620 reference PMID:22641620 evidence type PRIMARY_EXPERIMENT notes Characterization of linear tris-hydroxamate desferrioxamine complexation with Ni(II) in aqueous solution.
copper(2+) OTHER BINDS Coordination of divalent copper(2+) in aqueous solution (log beta110 ~ 14.1, measured in vitro only).			PMID:22641620 reference PMID:22641620 evidence type PRIMARY_EXPERIMENT notes Characterization of linear tris-hydroxamate desferrioxamine complexation with Cu(II) in aqueous solution.
zinc(2+) OTHER BINDS Coordination of divalent zinc(2+) in aqueous solution (log beta110 ~ 10.1, measured in vitro only).			PMID:22641620 reference PMID:22641620 evidence type PRIMARY_EXPERIMENT notes Characterization of linear tris-hydroxamate desferrioxamine complexation with Zn(II) in aqueous solution.

Explore across X-Mech

AntibioticMech (desferrioxamine D1) ↗ MediaIngredientMech (CHEBI:50456) ↗ TaxonMech: Streptomyces coelicolor A3(2) (NCBITaxon:100226) ↗ TaxonMech: Streptomyces coelicolor A3(2) (NCBITaxon:100226) ↗ PathwayMech (mibig:BGC0000940) ↗

Provenance

Source concept	Source	Version
CHEBI:50456	CHEBI	3-star

This page is generated from data/natural_products/fatty_acids/desferrioxamine-d1.yaml, which is generated from the committed inventories. Neither is edited by hand.