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HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound TOY

Identifiers

  • Canonical SMILES: 
    NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O)[C@H]2O)[C@H](N)C[C@@H]1O
  • IUPAC name: 
    (1S,2S,3R,4S,6R)-4,6-diamino-3-[(2,6-diamino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl)oxy]-2-hydroxycyclohexyl 3-amino-3-deoxy-alpha-D-glucopyranoside
  • InChi: 
    InChI=1S/C18H37N5O9/c19-3-9-8(25)2-7(22)17(29-9)31-15-5(20)1-6(21)16(14(15)28)32-18-13(27)11(23)12(26)10(4-24)30-18/h5-18,24-28H,1-4,19-23H2/t5-,6+,7+,8-,9+,10+,11-,12+,13+,14-,15+,16-,17+,18+/m0/s1
  • InChiKey: 
    NLVFBUXFDBBNBW-PBSUHMDJSA-N
  • SMARTS: 
    [#7]-[#6]-[#6@H]1-[#8]-[#6@H](-[#8]-[#6@@H]2-[#6@@H](-[#7])-[#6]-[#6@@H](-[#7])-[#6@H](-[#8]-[#6@H]3-[#8]-[#6@H](-[#6]-[#8])-[#6@@H](-[#8])-[#6@H](-[#7])-[#6@H]-3-[#8])-[#6@H]-2-[#8])-[#6@H](-[#7])-[#6]-[#6@@H]-1-[#8]

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

PubChem Logo 36294 ChEMBL Logo CHEMBL1747 PDB Logo TOY DrugBank Logo DB00684

RNA-SM complexes

PDB code Deposition date Reference publication
1lc4 April 5, 2002 Vicens Quentin, Westhof Eric. 2002. Crystal Structure of a Complex between the Aminoglycoside Tobramycin and an Oligonucleotide Containing the Ribosomal Decoding A Site Chemistry & Biology
1lc4 April 5, 2002 Vicens Quentin, Westhof Eric. 2002. Crystal Structure of a Complex between the Aminoglycoside Tobramycin and an Oligonucleotide Containing the Ribosomal Decoding A Site Chemistry & Biology
4lfc June 26, 2013 No publication
9hro Dec. 18, 2024 Duchardt-Ferner Elke, Kraus Leon, Limouchi Anahita, Suess Beatrix, Wöhnert Jens. 2025. Structural basis for ligand recognition in the tobramycin riboswitch Nucleic Acids Research

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 467.26 g/mol
HBA 14
HBD 10
HBA + HBD
AlogP -6.30
TPSA 268.17
RB 6

Radar chart