HARIBOSS logo

HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound DCP

Identifiers

  • Canonical SMILES: 
    NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2
  • IUPAC name: 
    2'-deoxycytidine 5'-(tetrahydrogen triphosphate)
  • InChi: 
    InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
  • InChiKey: 
    RGWHQCVHVJXOKC-SHYZEUOFSA-N
  • SMARTS: 
    [#7]-[#6]1:[#7]:[#6](=[#8]):[#7](:[#6]:[#6]:1)-[#6@H]1-[#6]-[#6@H](-[#8])-[#6@@H](-[#6]-[#8]-[#15@](-[#8])(=[#8])-[#8]-[#15@](-[#8])(=[#8])-[#8]-[#15](-[#8])(-[#8])=[#8])-[#8]-1

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

PubChem Logo 65091 ChEMBL Logo CHEMBL560403 PDB Logo DCP DrugBank Logo DB03258

RNA-SM complexes

PDB code Deposition date Reference publication
3ola Aug. 25, 2010 Gong Peng, Peersen Olve B.. 2010. Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase Proceedings of the National Academy of Sciences
3ola Aug. 25, 2010 Gong Peng, Peersen Olve B.. 2010. Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase Proceedings of the National Academy of Sciences
6wox April 26, 2020 Mäkinen Janne J., Shin Yeonoh, Vieras Eeva, Virta Pasi, Metsä-Ketelä Mikko, Murakami Katsuhiko S., Belogurov Georgiy A.. 2021. The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases Nature Communications
7n2m May 29, 2021 Baranovskiy Andrey G., Babayeva Nigar D., Lisova Alisa E., Morstadt Lucia M., Tahirov Tahir H.. 2022. Structural and functional insight into mismatch extension by human DNA polymerase α Proceedings of the National Academy of Sciences
8ub7 Sept. 22, 2023 Handa Sumit, Biswas Tapan, Chakraborty Jeet, Ghosh Gourisankar, Paul Blair G., Ghosh Partho. 2025. RNA control of reverse transcription in a diversity-generating retroelement Nature

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 466.99 g/mol
HBA 11
HBD 6
HBA + HBD
AlogP -1.18
TPSA 250.19
RB 8

Radar chart