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Harnessing RIBOnucleic acid - Small molecules Structures

Compound C5P

Identifiers

  • Canonical SMILES: 
    NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
  • IUPAC name: 
    5'-cytidylic acid
  • InChi: 
    InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
  • InChiKey: 
    IERHLVCPSMICTF-XVFCMESISA-N
  • SMARTS: 
    [#7]-[#6]1:[#7]:[#6](=[#8]):[#7](:[#6]:[#6]:1)-[#6@@H]1-[#8]-[#6@H](-[#6]-[#8]-[#15](-[#8])(-[#8])=[#8])-[#6@@H](-[#8])-[#6@H]-1-[#8]

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

PubChem Logo 6131 ChEMBL Logo CHEMBL307679 PDB Logo C5P DrugBank Logo DB03403

RNA-SM complexes

PDB code Deposition date Reference publication
4m2z Aug. 5, 2013 Court Donald L., Gan Jianhua, Liang Yu-He, Shaw Gary X., Tropea Joseph E., Costantino Nina, Waugh David S., Ji Xinhua. 2013. RNase III: Genetics and Function; Structure and Mechanism Annual Review of Genetics
4m2z Aug. 5, 2013 Court Donald L., Gan Jianhua, Liang Yu-He, Shaw Gary X., Tropea Joseph E., Costantino Nina, Waugh David S., Ji Xinhua. 2013. RNase III: Genetics and Function; Structure and Mechanism Annual Review of Genetics
5a0v April 23, 2015 Pei Xue-Yuan, Bralley Patricia, Jones George H., Luisi Ben F.. 2015. Linkage of catalysis and 5′ end recognition in ribonuclease RNase J Nucleic Acids Research
6u7y Sept. 3, 2019 Zhang Wen, Kim Seohyun Chris, Tam Chun Pong, Lelyveld Victor S, Bala Saikat, Chaput John C, Szostak Jack W. 2021. Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization Nucleic Acids Research
6u7z Sept. 3, 2019 Zhang Wen, Kim Seohyun Chris, Tam Chun Pong, Lelyveld Victor S, Bala Saikat, Chaput John C, Szostak Jack W. 2021. Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization Nucleic Acids Research
8gs2 Sept. 4, 2022 Kato Kazuki, Okazaki Sae, Schmitt-Ulms Cian, Jiang Kaiyi, Zhou Wenyuan, Ishikawa Junichiro, Isayama Yukari, Adachi Shungo, Nishizawa Tomohiro, Makarova Kira S., Koonin Eugene V., Abudayyeh Omar O., Gootenberg Jonathan S., Nishimasu Hiroshi. 2022. RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease Science
9ljv Jan. 15, 2025 Wang De-Ping, Zhao Rong, Hu Wen-Shu, Li Hai-Ning, Cao Ji-Min, Zhou Xin, Xiang Ye. 2025. Structural insights into polymerase-catalyzed FAD capping of hepatitis C virus RNA Nature Communications

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 323.05 g/mol
HBA 8
HBD 5
HBA + HBD
AlogP -2.45
TPSA 177.36
RB 4

Radar chart