dibekacin

CHEBI:37945 ·resolve ·ANTIBACTERIAL ·EXACT SEEDED

A kanamycin that is kanamycin B lacking the 3- and 4-hydroxy groups on the 2,6-diaminosugar 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
ARO:0000016 ARO:0000016

Chemical structure

Computed structure properties
Molecular formula	C18H37N5O8
Charge	0
Average mass	451.521 Da
Monoisotopic mass	451.26421 Da
Source	ChEBI
InChIKey	JJCQSGDBDPYCEO-XVZSLQNASA-N

SMILES

NC[C@@H]1CC[C@@H](N)[C@@H](O[C@H]2[C@H](O)[C@@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O)[C@H](N)C[C@@H]2N)O1

InChI

InChI=1S/C18H37N5O8/c19-4-6-1-2-7(20)17(28-6)30-15-8(21)3-9(22)16(14(15)27)31-18-13(26)11(23)12(25)10(5-24)29-18/h6-18,24-27H,1-5,19-23H2/t6-,7+,8-,9+,10+,11-,12+,13+,14-,15+,16-,17+,18+/m0/s1

Also called

(1R,2S,3S,4R,6S)-4,6-diamino-3-(3-amino-3-deoxy-α-D-glucopyranosyloxy)-2-hydroxycyclohexyl 2,6-diamino-2,3,4,6-tetradeoxy-α-D-erythro-hexopyranoside (EXACT_SYNONYM)— chebi
3',4'-Dideoxykanamycin B (EXACT_SYNONYM)— chebi
DKM (EXACT_SYNONYM)— chebi
O-3-Amino-3-deoxy-alpha-D-glucopyranosyl-(1-4)-O-(2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl-(1-6))-2-deoxy-L-streptamine (EXACT_SYNONYM)— chebi
Panamicin (EXACT_SYNONYM)— chebi
Debecacin (EXACT_SYNONYM)— aro
Dibekacina (EXACT_SYNONYM)— aro
Dibekacine (EXACT_SYNONYM)— aro
Dibekacinum (EXACT_SYNONYM)— aro
Dideoxykanamycin B (EXACT_SYNONYM)— aro
Icacine (EXACT_SYNONYM)— aro
Kappati (EXACT_SYNONYM)— aro
Orbicin (EXACT_SYNONYM)— aro

Cross-references

Equivalent identifiers for this same structure in other resources.

ARO:0000007
cas:34493-98-6
drugcentral:855
kegg.drug:D07811
patent:CN101278900
patent:CN101575354
reaxys:1441606
chembl:CHEMBL560976
pubchem.compound:470999

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

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:0000007`	dibekacin	`antibioticmech:aro-ee607c0e7d`	2026-08-30
CHEBI	`CHEBI:37945`	dibekacin	`antibioticmech:chebi-9100b2d366`	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:0000007 (dibekacin); 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

65 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_INACTIVATION 60

ANTIBIOTIC_INACTIVATION
Determinant	ARO ID	Organism	Gene families	Evidence
AAC(2')-Ia	ARO:3002523	not organism-specific	—	ARO:3002523 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(2')-Ib	ARO:3002524	not organism-specific	—	ARO:3002524 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(2')-Ic	ARO:3002525	not organism-specific	—	ARO:3002525 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(2')-Id	ARO:3002526	not organism-specific	—	ARO:3002526 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(2')-Ie	ARO:3002527	not organism-specific	—	ARO:3002527 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(3)-IIIa	ARO:3002536	not organism-specific	—	ARO:3002536 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(3)-IIIb	ARO:3002537	not organism-specific	—	ARO:3002537 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(3)-IIa	ARO:3002533	not organism-specific	—	ARO:3002533 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(3)-IIb	ARO:3002534	not organism-specific	—	ARO:3002534 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(3)-IIc	ARO:3002535	not organism-specific	—	ARO:3002535 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(3)-IId	ARO:3004623	not organism-specific	—	ARO:3004623 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(3)-IIe	ARO:3004621	not organism-specific	—	ARO:3004621 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(3)-IIg	ARO:3005085	not organism-specific	—	ARO:3005085 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(3)-IVa	ARO:3002539	not organism-specific	—	ARO:3002539 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-29a	ARO:3002583	not organism-specific	—	ARO:3002583 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-29b	ARO:3002584	not organism-specific	—	ARO:3002584 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-I-48	ARO:3004638	not organism-specific	—	ARO:3004638 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-I30	ARO:3002588	not organism-specific	—	ARO:3002588 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-IIa	ARO:3002594	not organism-specific	—	ARO:3002594 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-IIb	ARO:3002595	not organism-specific	—	ARO:3002595 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-IIc	ARO:3002596	not organism-specific	—	ARO:3002596 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Ia	ARO:3002545	not organism-specific	—	ARO:3002545 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Iaa	ARO:3002571	not organism-specific	—	ARO:3002571 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Iad	ARO:3002572	not organism-specific	—	ARO:3002572 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Iae	ARO:3002573	not organism-specific	—	ARO:3002573 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Iaf	ARO:3002574	not organism-specific	—	ARO:3002574 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Iai	ARO:3002575	not organism-specific	—	ARO:3002575 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Iaj	ARO:3003677	not organism-specific	—	ARO:3003677 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Iak	ARO:3003199	not organism-specific	—	ARO:3003199 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Ian	ARO:3003200	not organism-specific	—	ARO:3003200 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Iap	ARO:3007204	not organism-specific	—	ARO:3007204 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Ic	ARO:3002549	not organism-specific	—	ARO:3002549 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Ie-APH(2'')-Ia bifunctional protein	ARO:3002597	not organism-specific	—	ARO:3002597 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-If	ARO:3002553	not organism-specific	—	ARO:3002553 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Ig	ARO:3002554	not organism-specific	—	ARO:3002554 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Ih	ARO:3002555	not organism-specific	—	ARO:3002555 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Ii	ARO:3002556	not organism-specific	—	ARO:3002556 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Iid	ARO:3002589	not organism-specific	—	ARO:3002589 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Iih	ARO:3002590	not organism-specific	—	ARO:3002590 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Ij	ARO:3002557	not organism-specific	—	ARO:3002557 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Ik	ARO:3002558	not organism-specific	—	ARO:3002558 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Il	ARO:3004635	not organism-specific	—	ARO:3004635 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Im	ARO:3004629	not organism-specific	—	ARO:3004629 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Ip	ARO:3002559	not organism-specific	—	ARO:3002559 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Iq	ARO:3002560	not organism-specific	—	ARO:3002560 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Ir	ARO:3002561	not organism-specific	—	ARO:3002561 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Is	ARO:3002562	not organism-specific	—	ARO:3002562 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Isa	ARO:3002563	not organism-specific	—	ARO:3002563 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-It	ARO:3002564	not organism-specific	—	ARO:3002564 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Iu	ARO:3002565	not organism-specific	—	ARO:3002565 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Iv	ARO:3002566	not organism-specific	—	ARO:3002566 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Iw	ARO:3002567	not organism-specific	—	ARO:3002567 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Ix	ARO:3002568	not organism-specific	—	ARO:3002568 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Iy	ARO:3002569	not organism-specific	—	ARO:3002569 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
AAC(6')-Iz	ARO:3002570	not organism-specific	—	ARO:3002570 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
ANT(2'')-Ia	ARO:3000230	not organism-specific	—	ARO:3000230 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
ANT(3'')-II-AAC(6')-IId bifunctional protein	ARO:3002598	not organism-specific	—	ARO:3002598 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
ANT(4')-Ia	ARO:3002623	not organism-specific	—	ARO:3002623 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
ANT(4')-Ib	ARO:3003905	not organism-specific	—	ARO:3003905 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
APH(2'')-If	ARO:3004191	not organism-specific	—	ARO:3004191 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)

ANTIBIOTIC_TARGET_ALTERATION 5

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:0000007 (dibekacin); database assertion, not a primary citation.)
rmtA	ARO:3000859	not organism-specific	—	ARO:3000859 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
rmtB	ARO:3000860	not organism-specific	—	ARO:3000860 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
rmtC	ARO:3000861	not organism-specific	—	ARO:3000861 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); database assertion, not a primary citation.)
sgm	ARO:3000862	not organism-specific	—	ARO:3000862 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000007 (dibekacin); 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.