bekanamycin   Click here for help

GtoPdb Ligand ID: 12182

Synonyms: kanamycin B | nebramycin V
Approved drug PDB Ligand
bekanamycin is an approved drug
Compound class: Natural product
Comment: Bekanamycin (also known as kanamycin B) is one of the fermentation congeners produced by Streptomyces kanamyceticus [1,3]. It has activity against Gram-positive and Gram-negative bacteria and belongs to the aminoglycoside class of antibacterial compounds.

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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 Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). 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 288.4
Molecular weight 483.25
XLogP -5.55
No. Lipinski's rules broken 2

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
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.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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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]2N)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)CO)O)N)O)O)O[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CN)O)O)N)N
InChI InChI=1S/C18H37N5O10/c19-2-6-11(26)12(27)9(23)17(30-6)32-15-4(20)1-5(21)16(14(15)29)33-18-13(28)8(22)10(25)7(3-24)31-18/h4-18,24-29H,1-3,19-23H2/t4-,5+,6+,7+,8-,9+,10+,11+,12+,13+,14-,15+,16-,17+,18+/m0/s1
InChI Key SKKLOUVUUNMCJE-FQSMHNGLSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
Classification Click here for help
Compound class Natural product
Approved drug? Yes
Approved drug? Yes.
IUPAC Name Click here for help
(2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(1R,2S,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-diol
International Nonproprietary Names Click here for help
INN number INN
2838 bekanamycin
Synonyms Click here for help
kanamycin B | nebramycin V
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Bekanamycin
Other databases
CAS Registry No. 4696-76-8 (source: Scifinder)
ChEBI CHEBI:28098
ChEMBL Ligand CHEMBL176
DrugBank Ligand DB13673
DrugCentral Ligand 1520
GtoPdb PubChem SID 472319304
PubChem CID 439318
RCSB PDB Ligand 9CS
Search Google for chemical match using the InChIKey SKKLOUVUUNMCJE-FQSMHNGLSA-N
Search Google for chemicals with the same backbone SKKLOUVUUNMCJE
Search PubMed clinical trials bekanamycin
Search PubMed titles bekanamycin
Search PubMed titles/abstracts bekanamycin
UniChem Compound Search for chemical match using the InChIKey SKKLOUVUUNMCJE-FQSMHNGLSA-N
UniChem Connectivity Search for chemical match using the InChIKey SKKLOUVUUNMCJE-FQSMHNGLSA-N

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MedChemExpress
Bekanamycin (links to external site)
Cat. No. HY-B1174