edeine D

antibioticmech:aro-1cc6dbd596 ·ANTIBACTERIAL ·MINTED SEEDED

Edeine D is a subtype of edeine similar to edeine A with the beta-tyr replaced by beta-phe-beta-ala. Edeines bind to the 30S subunit to block fMet-tRNA interaction at the P site, inhibiting protein synthesis and subsequent structure/function processes critical for life or replication. — PMID:70202

Machine-generated and unreviewed. Identity, structure and cross-references come straight from ChEBI's and CARD's own data; no curator has signed off on this record yet.

Classification

nonribosomal peptide antibioticsARO:3009657

Strictly broader compounds or drug classes this molecule belongs to.

nonribosomal peptide antibiotics ARO:3009657

Chemical structure

Computed structure properties
Molecular formula	C33H58N10O9
Charge	0
Average mass	738.9 Da
Monoisotopic mass	738.43882347 Da
Source	PubChem · retrieved 2026-08-29
InChIKey	FPJBIRIVZPUIOL-DDURVGIBSA-N

SMILES

C1=CC=C(C=C1)[C@@H](CN)C(=O)N([C@@H](CN)C(=O)N[C@H](CCC[C@@H]([C@@H](CC(=O)NC(=O)CNCCCNCCCCN)O)N)C(=O)O)C(=O)C[C@H](N)O

InChI

InChI=1S/C33H58N10O9/c34-12-4-5-13-39-14-7-15-40-20-29(47)42-28(46)16-26(44)23(37)10-6-11-24(33(51)52)41-31(49)25(19-36)43(30(48)17-27(38)45)32(50)22(18-35)21-8-2-1-3-9-21/h1-3,8-9,22-27,39-40,44-45H,4-7,10-20,34-38H2,(H,41,49)(H,51,52)(H,42,46,47)/t22-,23+,24-,25+,26-,27-/m1/s1

Cross-references

Identifiers for this same structure in other resources. An accession that lands on two different structures in this corpus is withheld from both rather than shown here, since it names at most one of them.

edeine DARO:3000135
pubchem.compound:170400

Source concepts

Every upstream concept that resolved to this record. The merge is the product: this is what shows ChEBI and CARD are describing the same structure.

Upstream concepts merged into this record
Source	Native ID	Label	Minted CURIE	Version
ARO	`ARO:3000135`	edeine D	`antibioticmech:aro-1cc6dbd596`	2026-08-30

Molecular targets

The molecular entity or process this compound acts on. Each target carries evidence — this is a mechanistic claim, not a classification.

30S ribosomal subunit P-site RIBOSOMAL_SUBUNIT DIRECT_BINDING_TARGET

ARO:3000756

CARD/ARO database assertion; target organism, strain, and assay are not specified. The 30S P-site is asserted as the target site. Evidence status: PRIMARY_EVIDENCE_NEEDED. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

ARO:3000756 (CARD/ARO asserts targeted_by_antibiotic ARO:3000135 (edeine D); database assertion, not a primary citation.)

Resistance mechanisms

2 source-backed resistance determinants or associations, with ARO grounding where reported. Grouped by reported mechanism type.

ANTIBIOTIC_INACTIVATION 1

ANTIBIOTIC_INACTIVATION
Determinant	ARO ID	Organism	Gene families	Evidence
EdeQ	ARO:3004063	not organism-specific	—	ARO:3004063 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000135 (edeine D); database assertion, not a primary citation.)

ANTIBIOTIC_TARGET_ALTERATION 1

ANTIBIOTIC_TARGET_ALTERATION
Determinant	ARO ID	Organism	Gene families	Evidence
Escherichia coli 16S rRNA mutation conferring resistance to edeine	ARO:3003223	not organism-specific	—	ARO:3003223 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000135 (edeine D); database assertion, not a primary citation.)

Curation history

SEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Seeded from data/raw/ inventories (ARO)
RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-08-31 · seed_from_sources
Re-seeded from updated data/raw/ inventories

Provenance

Seeded by scripts/seed_from_sources.py from the committed inventories in data/raw/. View the record (YAML).

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