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dibekacin   Click here for help

GtoPdb Ligand ID: 12134

Synonyms: 3',4'-dideoxykanamycin B | debecacin
Approved drug PDB Ligand
dibekacin is an approved drug
Compound class: Synthetic organic
Comment: Dibekacin is a semisynthetic derivative of bekanamycin (kanamycin B), with activity against Gram-positive and Gram-negative bacteria [1]. It 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 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 13
Hydrogen bond donors 9
Rotatable bonds 6
Topological polar surface area 247.94
Molecular weight 451.26
XLogP -4.78
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 NC[C@@H]1CC[C@H]([C@H](O1)O[C@@H]1[C@@H](N)C[C@H]([C@@H]([C@H]1O)O[C@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)N)O)N)N
Isomeric SMILES C1C[C@H]([C@H](O[C@@H]1CN)O[C@@H]1[C@H](C[C@H]([C@@H]([C@H]1O)O[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O)N)O)N)N)N
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
InChI Key JJCQSGDBDPYCEO-XVZSLQNASA-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/)
Bioactivity Comments
MIC for in vitro antibacterial activity against Staphylococcus aureus FDA 209P (0.78 μg/ml) and Escherichia coli (1.56 μg/ml) is similar to bekanamycin [1]. The same study found that dibekacin demonstrates activity against E. coli strains carrying the R factor (1.56-3.12 μg/ml) and against Pseudomonas aeruginosa (0.78-6.25 μg/ml), for which bekanamycin shows no activity.