arbekacin

CHEBI:37922 ·resolve ·ANTIBACTERIAL ·EXACT SEEDED

A kanamycin that is kanamycin B bearing an N-(2S)-4-amino-2-hydroxybutyryl group on the aminocyclitol ring. — ChEBI

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

aminoglycoside antibioticARO:0000016

Strictly broader compounds or drug classes this molecule belongs to.

CHEBI:24951 CHEBI:24951
CHEBI:47779 CHEBI:47779
ARO:0000016 ARO:0000016

Chemical structure

Computed structure properties
Molecular formula	C22H44N6O10
Charge	0
Average mass	552.626 Da
Monoisotopic mass	552.31189 Da
Source	ChEBI
InChIKey	MKKYBZZTJQGVCD-XTCKQBCOSA-N

SMILES

NCC[C@H](O)C(=O)N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)CC[C@H]2N)[C@H](O)[C@H]1O[C@H]1O[C@H](CO)[C@@H](O)[C@H](N)[C@H]1O

InChI

InChI=1S/C22H44N6O10/c23-4-3-12(30)20(34)28-11-5-10(26)18(37-21-9(25)2-1-8(6-24)35-21)17(33)19(11)38-22-16(32)14(27)15(31)13(7-29)36-22/h8-19,21-22,29-33H,1-7,23-27H2,(H,28,34)/t8-,9+,10-,11+,12-,13+,14-,15+,16+,17-,18+,19-,21+,22+/m0/s1

Also called

(2S)-4-amino-N-[(1R,2S,3S,4R,5S)-5-amino-2-(3-amino-3-deoxy-α-D-glucopyranosyloxy)-4-(2,6-diamino-2,3,4,6-tetradeoxy-α-D-erythro-hexopyranosyloxy)-3-hydroxycyclohexyl]-2-hydroxybutanamide (EXACT_SYNONYM)— chebi
ABK (EXACT_SYNONYM)— chebi
habekacin (EXACT_SYNONYM)— aro
haberacin (EXACT_SYNONYM)— aro

Cross-references

Equivalent identifiers for this same structure in other resources.

ARO:3000654
cas:51025-85-5
drugbank:DB06696
drugcentral:235
kegg.drug:D07462
patent:DE2350169
patent:EP2199280
patent:US4107424
reaxys:5895351
chembl:CHEMBL426926
pubchem.compound:68682

Activity roles

Every antimicrobial role a source asserts for this compound — the unreduced evidence behind its antimicrobial_class.

CHEBI:33281 CHEBI:33281
CHEBI:33282 CHEBI:33282
CHEBI:36047 CHEBI:36047

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:3000654`	arbekacin	`antibioticmech:aro-0a5f8f9f83`	2026-08-30
CHEBI	`CHEBI:37922`	arbekacin	`antibioticmech:chebi-48c937767e`	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.

antibiotic sensitive 16S rRNA NUCLEIC_ACID DIRECT_BINDING_TARGET

ARO:3000755

CARD/ARO database assertion; target organism, strain, and assay are not specified. 16S rRNA is asserted as the target. Evidence status: PRIMARY_EVIDENCE_NEEDED. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

ARO:3000755 (CARD/ARO asserts targeted_by_antibiotic ARO:3000654 (arbekacin); database assertion, not a primary citation.)

Mechanism summary

Mode of action: PROTEIN_SYNTHESIS_INHIBITION host shared target — Assigned from ChEBI role CHEBI:48001 (protein synthesis inhibitor). ChEBI asserts the role on the compound. The target it names is one the host has too, so the mechanism is true but is not evidence of selectivity — see mode_of_action_target_scope. Not a curator's mechanistic review.

Resistance mechanisms

9 known routes by which microbes resist this compound, grounded in ARO where CARD models them. Grouped by mechanism type — expand a group to see its determinants.

ANTIBIOTIC_TARGET_ALTERATION 8

ANTIBIOTIC_TARGET_ALTERATION
Determinant	ARO ID	Organism	Gene families	Evidence
armA	ARO:3000858	not organism-specific	—	ARO:3000858 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000654 (arbekacin); database assertion, not a primary citation.)
rmtA	ARO:3000859	not organism-specific	—	ARO:3000859 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000654 (arbekacin); database assertion, not a primary citation.)
rmtB	ARO:3000860	not organism-specific	—	ARO:3000860 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000654 (arbekacin); database assertion, not a primary citation.)
rmtC	ARO:3000861	not organism-specific	—	ARO:3000861 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000654 (arbekacin); database assertion, not a primary citation.)
rmtD	ARO:3002667	not organism-specific	—	ARO:3002667 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000654 (arbekacin); database assertion, not a primary citation.)
rmtG	ARO:3002668	not organism-specific	—	ARO:3002668 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000654 (arbekacin); database assertion, not a primary citation.)
rmtH	ARO:3003198	not organism-specific	—	ARO:3003198 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000654 (arbekacin); database assertion, not a primary citation.)
sgm	ARO:3000862	not organism-specific	—	ARO:3000862 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000654 (arbekacin); database assertion, not a primary citation.)

ANTIBIOTIC_EFFLUX 1

ANTIBIOTIC_EFFLUX
Determinant	ARO ID	Organism	Gene families	Evidence
MexXY-OprA	ARO:3003038	not organism-specific	—	ARO:3003038 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000654 (arbekacin); database assertion, not a primary citation.)

Curation history

SEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Seeded from data/raw/ inventories (ARO, CHEBI)
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.