HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound AKN

Identifiers

  • Canonical SMILES: 
    NCC[C@H](O)C(=O)N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O
  • IUPAC name: 
    (2S)-4-amino-N-{(1R,2S,3S,4R,5S)-5-amino-2-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-4-[(6-amino-6-deoxy-alpha-D-glucopyranosyl)oxy]-3-hydroxycyclohexyl}-2-hydroxybutanamide
  • InChi: 
    InChI=1S/C22H43N5O13/c23-2-1-8(29)20(36)27-7-3-6(25)18(39-22-16(34)15(33)13(31)9(4-24)37-22)17(35)19(7)40-21-14(32)11(26)12(30)10(5-28)38-21/h6-19,21-22,28-35H,1-5,23-26H2,(H,27,36)/t6-,7+,8-,9+,10+,11-,12+,13+,14+,15-,16+,17-,18+,19-,21+,22+/m0/s1
  • InChiKey: 
    LKCWBDHBTVXHDL-RMDFUYIESA-N

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

37768 CHEMBL177 DB00479

RNA-SM complexes

PDB code Deposition date Reference publication
4p20 Feb. 28, 2014 KONDO J, FRANCOIS B, RUSSELL R, MURRAY J, WESTHOF E. . Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the γ-amino-α-hydroxybutyryl (haba) group Biochimie
4p20 Feb. 28, 2014 KONDO J, FRANCOIS B, RUSSELL R, MURRAY J, WESTHOF E. . Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the γ-amino-α-hydroxybutyryl (haba) group Biochimie
6ypu April 16, 2020 Nicholson David, Edwards Thomas A., O'Neill Alex J., Ranson Neil A.. . Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics Structure
8ev6 Oct. 19, 2022 Seely Savannah M., Parajuli Narayan P., De Tarafder Arindam, Ge Xueliang, Sanyal Suparna, Gagnon Matthieu G.. . Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome Nature Communications
8ev6 Oct. 19, 2022 Seely Savannah M., Parajuli Narayan P., De Tarafder Arindam, Ge Xueliang, Sanyal Suparna, Gagnon Matthieu G.. . Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome Nature Communications
8ev6 Oct. 19, 2022 Seely Savannah M., Parajuli Narayan P., De Tarafder Arindam, Ge Xueliang, Sanyal Suparna, Gagnon Matthieu G.. . Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome Nature Communications
8ev6 Oct. 19, 2022 Seely Savannah M., Parajuli Narayan P., De Tarafder Arindam, Ge Xueliang, Sanyal Suparna, Gagnon Matthieu G.. . Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome Nature Communications
8syl May 25, 2023 Seely Savannah M., Parajuli Narayan P., De Tarafder Arindam, Ge Xueliang, Sanyal Suparna, Gagnon Matthieu G.. . Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome Nature Communications
8syl May 25, 2023 Seely Savannah M., Parajuli Narayan P., De Tarafder Arindam, Ge Xueliang, Sanyal Suparna, Gagnon Matthieu G.. . Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome Nature Communications

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 585.29 g/mol
HBA 17
HBD 13
HBA + HBD
AlogP -8.42
TPSA 331.94
RB 10

Radar chart