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Compound Detail

CHEMBL176

BEKANAMYCIN
🧪 Phase III
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🧪 Phase III
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](N)[C@@H](O)[C@@H]1O
ChEMBL ↗ Properties Compare Identifier

Basic Information

ChEMBL ID CHEMBL176
Name BEKANAMYCIN
Phase Phase III
Structure Type MOL
InChI Key SKKLOUVUUNMCJE-FQSMHNGLSA-N

Known Names

Bekanamicina Bekanamycin Bekanamycine Kanamycin b Nebramycin v NK 1006 NK-1006
5
Targets
18
Activities
3
Assay Types
0
PK Parameters
20
Publications
7
Known Names
2
Indications
1
Mechanisms

Molecular Properties

483.5
MW (Da)
-7.33
ALogP
15
HBA
11
HBD
288.4
PSA (Ų)
0.17
QED
2
Ro5 Violations
6
Rot. Bonds

Drug Information

Molecule Type Small molecule
Chirality Single Enantiomer

Flags

Natural Product
USAN Stem -mycin

Extended Properties

Molecular Formula C18H37N5O10
MW 483.52
Aromatic Rings 0
Heavy Atoms 33
NP-Likeness 1.37

Mechanism of Action

Mechanism Action Type Target Direct Efficacy
Bacterial 70S ribosome inhibitor INHIBITOR Bacterial 70S ribosome ✓ ✓

Indications

Bacterial Infections Osteomyelitis

ATC Classification

J01GB13
bekanamycin
Level 1: ANTIINFECTIVES FOR SYSTEMIC USE
Level 2: ANTIBACTERIALS FOR SYSTEMIC USE

Activity Summary

IC50 8 meas. best 7.4
Kd 8 meas. best 7.22
EC50 2 meas. best 6.52

Target Activity Profile

Target Type Best pChEMBL Mean pChEMBL Best (nM) # Data
Ribosomal RNA A-site
CHEMBL614640
 IC50 7.4 7.4 40.0 1
Nucleic Acid
CHEMBL345
 Kd 7.22 5.8517 60.0 6
Nucleic Acid
CHEMBL345
 EC50 6.52 6.52 300.0 2
Ribosomal RNA A-site
CHEMBL614640
 Kd 5.85 5.85 1400.0 1
Beta-ketoacyl-[acyl-carrier-protein] synthase III
CHEMBL4914
 IC50 5.25 5.25 5600.0 1
3-oxoacyl-[acyl-carrier-protein] synthase 3
CHEMBL1795135
 IC50 5.2 5.2 6300.0 1
Unchecked
CHEMBL612545
 IC50 5.2 4.87 6300.0 2

Activity Data Samples

Top measurements by pChEMBL value

Target Type Rel. Value Units pChEMBL Assay PubMed
Ribosomal RNA A-site IC50 = 40.0 nM 7.4 Binding affinity to 16S rRNA A-site in Escherichia coli S30 extract assessed as ... 27509271
Nucleic Acid Kd = 60.0 nM 7.22 Binding affinity to A-site RNA 19445516
Nucleic Acid EC50 = 300.0 nM 6.52 Binding affinity to Escherichia coli 16S rRNA helix 44 assessed as stabilization... 19946275
Nucleic Acid EC50 = 300.0 nM 6.52 Binding affinity to Escherichia coli 23S rRNA assessed as stabilization of class... 19946275
Nucleic Acid Kd = 910.0 nM 6.04 Tested for binding affinity against RNA construct E 11814798
Ribosomal RNA A-site Kd = 1400.0 nM 5.85 Binding affinity of aminoglycoside to 16S ribosomal RNA A-site in Escherichia co... 11206440
Nucleic Acid Kd = 2750.0 nM 5.56 Tested for binding affinity against RNA construct D 11814798
Nucleic Acid Kd = 2900.0 nM 5.54 Tested for binding affinity against RNA construct B 11814798
Nucleic Acid Kd = 2950.0 nM 5.53 Tested for binding affinity against RNA construct A 11814798
Beta-ketoacyl-[acyl-carrier-protein] synthase III IC50 = 5600.0 nM 5.25 Inhibition of Escherichia coli FabH expressed in Escherichia coli DH10B using ho... -
Nucleic Acid Kd = 6000.0 nM 5.22 Displacement of ethidium bromide from human pre-hsa-mir-155 miRNA after 30 mins 22257890
3-oxoacyl-[acyl-carrier-protein] synthase 3 IC50 = 6300.0 nM 5.2 Inhibition of Escherichia coli FabH overexpressed in Escherichia coli DH10B cell... 24332628
Unchecked IC50 = 6300.0 nM 5.2 Inhibition of full-length N-terminal His-tagged Escherichia coli FabH expressed ... -
Unchecked IC50 = 28860.0 nM 4.54 Inhibition of cytosolic eukaryotic translation in rabbit reticulocyte S30 extrac... 27509271

Literature References

PubMed DOI Target Context # Activities
19946275 10.1038/nchembio.274 Nucleic Acid 11
26264847 10.1016/j.bmc.2015.07.062 Unchecked 11
26592740 10.1021/acs.jmedchem.5b01375 Candida albicans 8
26592740 10.1021/acs.jmedchem.5b01375 Unchecked 7
20145089 10.1128/aac.01444-09 Escherichia coli 7
26592740 10.1021/acs.jmedchem.5b01375 Staphylococcus aureus 6
11814798 10.1016/s0960-894x(01)00760-0 Nucleic Acid 5
107311 10.1021/jm00190a015 Pseudomonas aeruginosa 5
3543366 10.1021/jm00385a015 ADMET 4
107311 10.1021/jm00190a015 Escherichia coli 4
2016726 10.1021/jm00108a037 Serratia marcescens 3
21177112 10.1016/j.bmc.2010.11.065 Escherichia coli 3
21177112 10.1016/j.bmc.2010.11.065 Staphylococcus epidermidis 3
27509271 10.1021/acs.jmedchem.6b00793 Klebsiella pneumoniae 3
107311 10.1021/jm00190a015 Providencia rettgeri 2
26592740 10.1021/acs.jmedchem.5b01375 Listeria monocytogenes 2
16190754 10.1021/jm050368c Staphylococcus aureus 2
21177112 10.1016/j.bmc.2010.11.065 Staphylococcus aureus 2
107311 10.1021/jm00190a015 Staphylococcus aureus 2
2016724 10.1021/jm00108a035 Serratia marcescens 2

Data from ChEMBL 36 via Core Engine