desferrialbomycin δ2
CHEBI:83200 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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.
A member of the class of desferrialbomycins that is desferrialbomycin ε in which the hydrogen attached to the nitrogen at position 4 of the pyrimidone moiety is replaced by a carbamoyl group. The iron(III) complex of desferrialbomycin δ1 is the antibiotic albomycin δ2.
Structure
| Standard InChIKey | YXNKTOYTHKJHIU-RREKCFDTSA-N |
|---|---|
| SMILES | [H][C@]1([C@@H](O)[C@@H](NC(=O)[C@H](CO)NC(=O)[C@H](CCCN(O)C(C)=O)NC(=O)[C@H](CCCN(O)C(C)=O)NC(=O)[C@@H](N)CCCN(O)C(C)=O)C(=O)O)S[C@@]([H])(n2ccc(=NC(N)=O)n(C)c2=O)[C@H](O)[C@H]1O |
| Stereochemistry | fully defined |
Filing pathway
Amino acids and peptides — computed by NPClassifier npclassifier.gnps2.org@2026-10-31, which is why it is pinned rather than recomputed. The gene cluster's asserted class is nrps, 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 sp. Strain: ATCC 700974 NCBITaxon:1931 |
BGC_CHARACTERIZED | mibig:BGC0002300 | PMID:22704654
|
| Streptomyces griseus Strain: TÜ 6 NCBITaxon:1911 |
AXENIC_CULTURE | PMID:387415
|
Occurrences 0
None cited.
Biosynthetic gene clusters 1
| Accession | Host | Locus evidence | Genome |
|---|---|---|---|
| mibig:BGC0002300 | Streptomyces sp. NCBITaxon:1931 |
CLUSTER_DEMONSTRATED | genbank:JN252488.1 |
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 | AbmA-AbmR biosynthetic enzymes (mibig:BGC0002300) | CHEBI:15729 + CHEBI:17115 + CHEBI:16704 + CHEBI:15351 → CHEBI:83200 | PMID:22704654 |
Step 1: Biosynthesis of the 6'-amino-4'-thioheptose nucleoside warhead (SB-217452) from uridine and L-serine, coupled to the N-terminal tri-N5-acetyl-N5-hydroxy-L-ornithine siderophore peptide to yield desferrialbomycin delta2.
Mechanism & Biosynthesis Overview
Causal graph — bioactivity 9 nodes, 8 edges
Biosynthesis of the Trojan-horse peptidyl-nucleoside sideromycin desferrialbomycin delta2 via the abmA-R cluster (mibig:BGC0002300) in Streptomyces sp. ATCC 700974, trihydroxamate chelation of Fe(III), and active uptake via bacterial FhuA and FhuD.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| L-ornithine | substrate_of | abmA-R biosynthetic gene cluster | Supplies the three N5-acetyl-N5-hydroxy-L-ornithine residues of the siderophore cap. | PMID:22704654
|
| L-serine | substrate_of | abmA-R biosynthetic gene cluster | Provides the L-seryl linker between the trihydroxamate peptide and the thionucleoside warhead. | PMID:22704654
|
| uridine | substrate_of | abmA-R biosynthetic gene cluster | Precursor of the N4-carbamoyl-3-methylcytidine thionucleoside warhead. | PMID:22704654
|
| abmA-R biosynthetic gene cluster | synthesizes | desferrialbomycin δ2 | Produces metal-free desferrialbomycin delta2. | PMID:22704654
|
| desferrialbomycin δ2 | chelates | iron(3+) | Trihydroxamate peptide cap coordinates ferric iron(3+) to form albomycin delta2. | PMID:10850805
|
| desferrialbomycin δ2 | binds | Outer membrane transporter FhuA | In its ferric-complexed form (albomycin delta2), desferrialbomycin delta2 binds the E. coli outer membrane receptor FhuA. | PMID:10850805
|
| Outer membrane transporter FhuA | transfers_to | Periplasmic binding protein FhuD | Translocates ferric-albomycin into the periplasm for capture by FhuD. | PMID:10742172
|
| Periplasmic binding protein FhuD | enables | siderophore transport | Mediates Trojan-horse import into the bacterial cytoplasm where peptidase N releases the seryl-tRNA synthetase inhibitor warhead. | PMID:387415
|
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 Hexadentate octahedral coordination of ferric iron(3+) via the N-terminal tri-N5-acetyl-N5-hydroxy-L-ornithine peptide carrier moiety to form the active Trojan-horse sideromycin albomycin delta2. |
PMID:22704654 |
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Provenance
| Source concept | Source | Version |
|---|---|---|
| CHEBI:83200 | CHEBI | 3-star |
This page is generated from data/natural_products/amino_acids_and_peptides/desferrialbomycin-2.yaml, which is generated from the committed inventories. Neither is edited by hand.