HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound TPP

Identifiers

  • Canonical SMILES: 
    Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
  • IUPAC name: 
    3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium
  • InChi: 
    InChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1
  • InChiKey: 
    AYEKOFBPNLCAJY-UHFFFAOYSA-O

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

1132 CHEMBL1236376

RNA-SM complexes

PDB code Deposition date Reference publication
2cky April 24, 2006 Thore Stéphane, Leibundgut Marc, Ban Nenad. . Structure of the Eukaryotic Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand Science
2cky April 24, 2006 Thore Stéphane, Leibundgut Marc, Ban Nenad. . Structure of the Eukaryotic Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand Science
2gdi March 16, 2006 Serganov Alexander, Polonskaia Anna, Phan Anh Tuân, Breaker Ronald R., Patel Dinshaw J.. . Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch Nature
2gdi March 16, 2006 Serganov Alexander, Polonskaia Anna, Phan Anh Tuân, Breaker Ronald R., Patel Dinshaw J.. . Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch Nature
2hoj July 14, 2006 Edwards Thomas E., Ferré-D'Amaré Adrian R.. . Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition Structure
2hol July 14, 2006 Edwards Thomas E., Ferré-D'Amaré Adrian R.. . Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition Structure
3d2g May 8, 2008 Thore Stéphane, Frick Christian, Ban Nenad. . Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch Journal of the American Chemical Society
3d2g May 8, 2008 Thore Stéphane, Frick Christian, Ban Nenad. . Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch Journal of the American Chemical Society
3k0j Sept. 24, 2009 Kulshina Nadia, Edwards Thomas E., Ferré-D'Amaré Adrian R.. . Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch RNA
3k0j Sept. 24, 2009 Kulshina Nadia, Edwards Thomas E., Ferré-D'Amaré Adrian R.. . Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch RNA
7tda Dec. 30, 2021 Zeller Meredith J., Nuthanakanti Ashok, Li Kelin, Aubé Jeffrey, Serganov Alexander, Weeks Kevin M.. . Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery ACS Chemical Biology
9c6k June 7, 2024 Haack Daniel B., Rudolfs Boris, Jin Shouhong, Khitun Alexandra, Weeks Kevin M., Toor Navtej. . Scaffold-enabled high-resolution cryo-EM structure determination of RNA Nature Communications

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 425.04 g/mol
HBA 8
HBD 4
HBA + HBD
AlogP 0.84
TPSA 168.97
RB 8

Radar chart