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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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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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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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

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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
References
1. Dijkstra JA, van der Laan T, Akkerman OW, Bolhuis MS, de Lange WCM, Kosterink JGW, van der Werf TS, Alffenaar JWC, van Soolingen D. (2018)
In Vitro Susceptibility of Mycobacterium tuberculosis to Amikacin, Kanamycin, and Capreomycin.
Antimicrob Agents Chemother, 62 (3). [PMID:29311078]
2. UMEZAWA H, UEDA M, MAEDA K, YAGISHITA K, KONDO S, OKAMI Y, UTAHARA R, OSATO Y, NITTA K, TAKEUCHI T. (1957)
Production and isolation of a new antibiotic: kanamycin.
J Antibiot (Tokyo), 10 (5): 181-8. [PMID:13513509]