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Harnessing RIBOnucleic acid - Small molecules Structures

Compound CH1

Identifiers

  • Canonical SMILES: 
    NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)C[C@H]2O
  • IUPAC name: 
    3'-deoxycytidine 5'-(tetrahydrogen triphosphate)
  • InChi: 
    InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-6(13)3-5(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: 
    CHKFLBOLYREYDO-SHYZEUOFSA-N
  • SMARTS: 
    [#7]-[#6]1:[#7]:[#6](=[#8]):[#7](:[#6]:[#6]:1)-[#6@@H]1-[#8]-[#6@H](-[#6]-[#8]-[#15@@](-[#8])(=[#8])-[#8]-[#15@@](-[#8])(=[#8])-[#8]-[#15](-[#8])(-[#8])=[#8])-[#6]-[#6@H]-1-[#8]

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

PubChem Logo 153054 ChEMBL Logo CHEMBL480328 PDB Logo CH1

RNA-SM complexes

PDB code Deposition date Reference publication
1n1h Oct. 17, 2002 Tao Yizhi, Farsetta Diane L., Nibert Max L., Harrison Stephen C.. 2002. RNA Synthesis in a Cage—Structural Studies of Reovirus Polymerase λ3 Cell
1n35 Oct. 25, 2002 Tao Yizhi, Farsetta Diane L., Nibert Max L., Harrison Stephen C.. 2002. RNA Synthesis in a Cage—Structural Studies of Reovirus Polymerase λ3 Cell
1uon Sept. 21, 2003 Zhang Xing, Walker Stephen B, Chipman Paul R, Nibert Max L, Baker Timothy S. 2003. Reovirus polymerase λ3 localized by cryo-electron microscopy of virions at a resolution of 7.6 Å Nature Structural & Molecular Biology
3avy March 8, 2011 Takeshita Daijiro, Tomita Kozo. 2012. Molecular basis for RNA polymerization by Qβ replicase Nature Structural & Molecular Biology
3vnv Jan. 18, 2012 Takeshita Daijiro, Yamashita Seisuke, Tomita Kozo. 2012. Mechanism for Template-Independent Terminal Adenylation Activity of Qβ Replicase Structure
6woy 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
9mn9 Dec. 20, 2024 Herbine Karl, Nayak Ashok R., Zamudio-Ochoa Angelica, Temiakov Dmitry. 2025. Structural basis for promoter recognition and transcription factor binding and release in human mitochondria Molecular Cell

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