kanamycin   Click here for help

GtoPdb Ligand ID: 12132

Synonyms: kanamycin A
Approved drug PDB Ligand
kanamycin is an approved drug (FDA (1973))
Compound class: Natural product
Comment: Kanamycin (also known as kanamycin A) is the main fermentation product of Streptomyces kanamyceticus [2]. Additional products have been subsequently identified, including bekanamycin (kanamycin B), kanamycin C (PubChem CID: 439582), kanamycin D (PubChem CID: 10368104) and kanamycin X (PubChem CID: 25202222).
Kanamycin has activity against Gram-positive and Gram-negative bacteria and belongs to the aminoglycoside class of antibacterial compounds.
2D Structure
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Physico-chemical Properties
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Hydrogen bond acceptors 15
Hydrogen bond donors 11
Rotatable bonds 6
Topological polar surface area 282.61
Molecular weight 484.24
XLogP -5.49
No. Lipinski's rules broken 2
SMILES / InChI / InChIKey
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Canonical SMILES OC[C@H]1O[C@H](O[C@H]2[C@H](N)C[C@@H]([C@H]([C@@H]2O)O[C@H]2O[C@H](CN)[C@H]([C@@H]([C@H]2O)O)O)N)[C@@H]([C@H]([C@@H]1O)N)O
Isomeric SMILES C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CN)O)O)O)O)O[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O)N)O)N
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
InChI Key SBUJHOSQTJFQJX-NOAMYHISSA-N
Classification Click here for help
Compound class Natural product
Approved drug? Yes (FDA (1973))
IUPAC Name Click here for help
(2R,3S,4S,5R,6R)-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-3-[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2-hydroxycyclohexyl]oxyoxane-3,4,5-triol
International Nonproprietary Names Click here for help
INN number INN
870 kanamycin
Synonyms Click here for help
kanamycin A
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Kanamycin
Other databases
CAS Registry No. 59-01-8 (source: Scifinder)
ChEBI CHEBI:17630
ChEMBL Ligand CHEMBL1384
DrugBank Ligand DB01172
DrugCentral Ligand 1519
GtoPdb PubChem SID 472319254
PubChem CID 6032
RCSB PDB Ligand KAN
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UniChem Compound Search for chemical match using the InChIKey SBUJHOSQTJFQJX-NOAMYHISSA-N
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Wikipedia Kanamycin A