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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
  • SMARTS: 
    [#6]-[#6]1:[#7]:[#6]:[#6](-[#6]-[#7+]2:[#6]:[#16]:[#6](-[#6]-[#6]-[#8]-[#15@@](-[#8])(=[#8])-[#8]-[#15](-[#8])(-[#8])=[#8]):[#6]:2-[#6]):[#6](-[#7]):[#7]:1

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

PubChem Logo 1132 ChEMBL Logo CHEMBL1236376 PDB Logo TPP

RNA-SM complexes

PDB code Deposition date Reference publication
2cky April 24, 2006 Thore Stéphane, Leibundgut Marc, Ban Nenad. 2006. Structure of the Eukaryotic Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand Science
2cky April 24, 2006 Thore Stéphane, Leibundgut Marc, Ban Nenad. 2006. 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.. 2006. 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.. 2006. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch Nature
2hoj July 14, 2006 Edwards Thomas E., Ferré-D'Amaré Adrian R.. 2006. 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.. 2006. 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. 2008. 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. 2008. 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.. 2010. 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.. 2010. 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.. 2022. 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. 2025. 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