kanamycin A

CHEBI:17630 ·resolve ·ANTIBACTERIAL ·EXACT SEEDED

Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. — PMID:10103173

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	C18H36N4O11
Charge	0
Average mass	484.503 Da
Monoisotopic mass	484.23806 Da
Source	ChEBI
InChIKey	SBUJHOSQTJFQJX-NOAMYHISSA-N

SMILES

NC[C@H]1O[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)[C@H](O)[C@@H](O)[C@@H]1O

InChI

InChI=1S/C18H36N4O11/c19-2-6-10(25)12(27)13(28)18(30-6)33-16-5(21)1-4(20)15(14(16)29)32-17-11(26)8(22)9(24)7(3-23)31-17/h4-18,23-29H,1-3,19-22H2/t4-,5+,6-,7-,8+,9-,10-,11-,12+,13-,14-,15+,16-,17-,18-/m1/s1

Also called

(1S,2R,3R,4S,6R)-4,6-diamino-3-(6-amino-6-deoxy-α-D-glucopyranosyloxy)-2-hydroxycyclohexyl 3-amino-3-deoxy-α-D-glucopyranoside (EXACT_SYNONYM)— chebi
4,6-diamino-2-hydroxy-1,3-cyclohexane 3,6'diamino-3,6'-dideoxydi-α-D-glucoside (EXACT_SYNONYM)— chebi
4,6-diamino-2-hydroxy-1,3-cyclohexylene 3,6'-diamino-3,6'-dideoxydi-D-glucopyranoside (EXACT_SYNONYM)— chebi
KANAMYCIN A (EXACT_SYNONYM)— chebi
Kanamycin A (EXACT_SYNONYM)— chebi
O-3-amino-3-deoxy-α-D-glucopyranosyl-(1→6)-O-(6-amino-6-deoxy-α-D-glucopyranosyl-(1→4))-2-deoxy-D-streptamine (EXACT_SYNONYM)— chebi
Aminodeoxykanamycin (EXACT_SYNONYM)— aro
Aspidium (EXACT_SYNONYM)— aro
Kanamicina (EXACT_SYNONYM)— aro
Kanamycin sulfate (EXACT_SYNONYM)— aro
Kanamycine (EXACT_SYNONYM)— aro
Kanamycinum (EXACT_SYNONYM)— aro
Kantrex (EXACT_SYNONYM)— aro
kanamycin (EXACT_SYNONYM)— aro

Cross-references

Equivalent identifiers for this same structure in other resources.

ARO:0000049
beilstein:61647
cas:59-01-8
drugbank:DB01172
drugcentral:1519
gmelin:2044856
kegg.compound:C01822
lincs.smallmolecule:LSM-5261
pdb-ccd:KAN
vsdb:1921
wikipedia.en:Kanamycin
chembl:CHEMBL223520
pubchem.compound:6032

Activity roles

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

CHEBI:33281 CHEBI:33281

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:0000049`	kanamycin A	`antibioticmech:aro-70a2160cf2`	2026-08-30
CHEBI	`CHEBI:17630`	kanamycin A	`antibioticmech:chebi-952d7701a7`	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:0000049 (kanamycin A); database assertion, not a primary citation.)

Resistance mechanisms

78 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 51

ANTIBIOTIC_INACTIVATION
Determinant	ARO ID	Organism	Gene families	Evidence
AAC(3)-IIIa	ARO:3002536	not organism-specific	—	ARO:3002536 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(3)-IIIb	ARO:3002537	not organism-specific	—	ARO:3002537 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(3)-Ib/AAC(6')-Ib3 bifunctional protein	ARO:3002600	not organism-specific	—	ARO:3002600 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(3)-Xa	ARO:3002544	not organism-specific	—	ARO:3002544 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-29a	ARO:3002583	not organism-specific	—	ARO:3002583 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-29b	ARO:3002584	not organism-specific	—	ARO:3002584 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-31	ARO:3002585	not organism-specific	—	ARO:3002585 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-34	ARO:3003989	not organism-specific	—	ARO:3003989 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-I-43	ARO:3004641	not organism-specific	—	ARO:3004641 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib	ARO:3002546	not organism-specific	—	ARO:3002546 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib-Hangzhou	ARO:3002592	not organism-specific	—	ARO:3002592 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib-SK	ARO:3002593	not organism-specific	—	ARO:3002593 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib-Suzhou	ARO:3002591	not organism-specific	—	ARO:3002591 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib-cr1	ARO:3002547	not organism-specific	—	ARO:3002547 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib-cr3	ARO:3005112	not organism-specific	—	ARO:3005112 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib-cr4	ARO:3005114	not organism-specific	—	ARO:3005114 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib-cr5	ARO:3005115	not organism-specific	—	ARO:3005115 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib-cr6	ARO:3005116	not organism-specific	—	ARO:3005116 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib-cr7	ARO:3005117	not organism-specific	—	ARO:3005117 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib-cr8	ARO:3005118	not organism-specific	—	ARO:3005118 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib-cr9	ARO:3005119	not organism-specific	—	ARO:3005119 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib10	ARO:3002581	not organism-specific	—	ARO:3002581 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib11	ARO:3002582	not organism-specific	—	ARO:3002582 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib3	ARO:3002576	not organism-specific	—	ARO:3002576 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib4	ARO:3002577	not organism-specific	—	ARO:3002577 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib7	ARO:3002578	not organism-specific	—	ARO:3002578 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib8	ARO:3002579	not organism-specific	—	ARO:3002579 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
AAC(6')-Ib9	ARO:3002580	not organism-specific	—	ARO:3002580 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); 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:0000049 (kanamycin A); database assertion, not a primary citation.)
ANT(2'')-Ia	ARO:3000230	not organism-specific	—	ARO:3000230 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(2'')-IIIa	ARO:3002636	not organism-specific	—	ARO:3002636 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(2'')-IVa	ARO:3002637	not organism-specific	—	ARO:3002637 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(2'')-Ie	ARO:3002634	not organism-specific	—	ARO:3002634 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(2'')-If	ARO:3004191	not organism-specific	—	ARO:3004191 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(2'')-Ig	ARO:3002669	not organism-specific	—	ARO:3002669 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(3')-IIIa	ARO:3002647	not organism-specific	—	ARO:3002647 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(3')-IIa	ARO:3002644	not organism-specific	—	ARO:3002644 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(3')-IIb	ARO:3002645	not organism-specific	—	ARO:3002645 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(3')-IIc	ARO:3002646	not organism-specific	—	ARO:3002646 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(3')-IVa	ARO:3002648	not organism-specific	—	ARO:3002648 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(3')-IXa	ARO:3004087	not organism-specific	—	ARO:3004087 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(3')-Ia	ARO:3002641	not organism-specific	—	ARO:3002641 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(3')-Ib	ARO:3002642	not organism-specific	—	ARO:3002642 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(3')-VIIIa	ARO:3004680	not organism-specific	—	ARO:3004680 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(3')-VIIIb	ARO:3004086	not organism-specific	—	ARO:3004086 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(3')-VIIa	ARO:3002654	not organism-specific	—	ARO:3002654 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(3')-VIa	ARO:3002652	not organism-specific	—	ARO:3002652 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
APH(3')-VIb	ARO:3002653	not organism-specific	—	ARO:3002653 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
aac(6')-Ib-cr10	ARO:3007770	not organism-specific	—	ARO:3007770 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
aac(6')-Ib-cr11	ARO:3007771	not organism-specific	—	ARO:3007771 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
aphA15	ARO:3004675	not organism-specific	—	ARO:3004675 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)

ANTIBIOTIC_TARGET_ALTERATION 20

ANTIBIOTIC_TARGET_ALTERATION
Determinant	ARO ID	Organism	Gene families	Evidence
Borreliella burgdorferi 16S rRNA mutation conferring resistance to kanamycin	ARO:3003503	not organism-specific	—	ARO:3003503 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to kanamycin A	ARO:3003399	not organism-specific	—	ARO:3003399 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
Kanamycin resistant whib7	ARO:3004966	not organism-specific	—	ARO:3004966 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
Mycobacterium tuberculosis 16S rRNA (rrnS) mutation conferring resistance to amikacin	ARO:3007536	not organism-specific	—	ARO:3007536 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to kanamycin	ARO:3003436	not organism-specific	—	ARO:3003436 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
Mycobacterium tuberculosis eis with mutation conferring resistance to kanamycin	ARO:3004963	not organism-specific	—	ARO:3004963 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
Mycobacterium tuberculosis whib7 mutations confer resistance to kanamycin	ARO:3004967	not organism-specific	—	ARO:3004967 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
Mycobacteroides abscessus 16S rRNA mutation conferring resistance to kanamycin	ARO:3003236	not organism-specific	—	ARO:3003236 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
Mycobacteroides chelonae 16S rRNA mutation conferring resistance to kanamycin A	ARO:3003515	not organism-specific	—	ARO:3003515 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
Mycolicibacterium smegmatis 16S rRNA (rrsA) mutation conferring resistance to kanamycin A	ARO:3003543	not organism-specific	—	ARO:3003543 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
Mycolicibacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to kanamycin A	ARO:3003542	not organism-specific	—	ARO:3003542 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
armA	ARO:3000858	not organism-specific	—	ARO:3000858 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
kamB	ARO:3004102	not organism-specific	—	ARO:3004102 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
rmtA	ARO:3000859	not organism-specific	—	ARO:3000859 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
rmtB	ARO:3000860	not organism-specific	—	ARO:3000860 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
rmtC	ARO:3000861	not organism-specific	—	ARO:3000861 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
rmtD2	ARO:3004677	not organism-specific	—	ARO:3004677 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
rmtE2	ARO:3004679	not organism-specific	—	ARO:3004679 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
rmtF	ARO:3002666	not organism-specific	—	ARO:3002666 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
sgm	ARO:3000862	not organism-specific	—	ARO:3000862 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)

ANTIBIOTIC_EFFLUX 5

ANTIBIOTIC_EFFLUX
Determinant	ARO ID	Organism	Gene families	Evidence
AcrAD-TolC	ARO:3004082	not organism-specific	—	ARO:3004082 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
Staphylococcus aureus LmrS	ARO:3004572	not organism-specific	—	ARO:3004572 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
acrD	ARO:3000491	not organism-specific	—	ARO:3000491 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
kdpDE	ARO:3004046	not organism-specific	—	ARO:3004046 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)
mdeA	ARO:3007011	not organism-specific	—	ARO:3007011 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)

REDUCED_PERMEABILITY 1

REDUCED_PERMEABILITY
Determinant	ARO ID	Organism	Gene families	Evidence
Escherichia coli mipA	ARO:3004127	not organism-specific	—	ARO:3004127 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); database assertion, not a primary citation.)

UNKNOWN 1

UNKNOWN
Determinant	ARO ID	Organism	Gene families	Evidence
PvrR	ARO:3003688	not organism-specific	—	ARO:3003688 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000049 (kanamycin A); 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.