HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound 2TM

Identifiers

  • Canonical SMILES: 
    NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
  • IUPAC name: 
    5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine
  • InChi: 
    InChI=1S/C10H18N3O13P3/c11-6-1-2-13(10(16)12-6)9-8(15)7(14)5(25-9)3-24-27(17,18)4-28(19,20)26-29(21,22)23/h1-2,5,7-9,14-15H,3-4H2,(H,17,18)(H,19,20)(H2,11,12,16)(H2,21,22,23)/t5-,7-,8-,9-/m1/s1
  • InChiKey: 
    STGUOVSTMBLHFT-ZOQUXTDFSA-N

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

73659181

RNA-SM complexes

PDB code Deposition date Reference publication
5x22 Jan. 29, 2017 Maffioli Sonia I., Zhang Yu, Degen David, Carzaniga Thomas, Del Gatto Giancarlo, Serina Stefania, Monciardini Paolo, Mazzetti Carlo, Guglierame Paola, Candiani Gianpaolo, Chiriac Alina Iulia, Facchetti Giuseppe, Kaltofen Petra, Sahl Hans-Georg, Dehò Gianni, Donadio Stefano, Ebright Richard H.. . Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase Cell
5x22 Jan. 29, 2017 Maffioli Sonia I., Zhang Yu, Degen David, Carzaniga Thomas, Del Gatto Giancarlo, Serina Stefania, Monciardini Paolo, Mazzetti Carlo, Guglierame Paola, Candiani Gianpaolo, Chiriac Alina Iulia, Facchetti Giuseppe, Kaltofen Petra, Sahl Hans-Georg, Dehò Gianni, Donadio Stefano, Ebright Richard H.. . Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase Cell
7eh0 March 27, 2021 Skalenko Kyle S., Li Lingting, Zhang Yuanchao, Vvedenskaya Irina O., Winkelman Jared T., Cope Alexander L., Taylor Deanne M., Shah Premal, Ebright Richard H., Kinney Justin B., Zhang Yu, Nickels Bryce E.. . Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli Proceedings of the National Academy of Sciences
7eh1 March 27, 2021 Skalenko Kyle S., Li Lingting, Zhang Yuanchao, Vvedenskaya Irina O., Winkelman Jared T., Cope Alexander L., Taylor Deanne M., Shah Premal, Ebright Richard H., Kinney Justin B., Zhang Yu, Nickels Bryce E.. . Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli Proceedings of the National Academy of Sciences
7mkn April 26, 2021 Qayyum M. Zuhaib, Molodtsov Vadim, Renda Andrew, Murakami Katsuhiko S.. . Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli Journal of Biological Chemistry
7mko April 26, 2021 Qayyum M. Zuhaib, Molodtsov Vadim, Renda Andrew, Murakami Katsuhiko S.. . Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli Journal of Biological Chemistry
7qtl Jan. 14, 2022 Kouba Tomas, Dubankova Anna, Drncova Petra, Donati Elisa, Vidossich Pietro, Speranzini Valentina, Pflug Alex, Huchting Johanna, Meier Chris, De Vivo Marco, Cusack Stephen. . Direct observation of backtracking by influenza A and B polymerases upon consecutive incorporation of the nucleoside analog T1106 Cell Reports
7vba Aug. 31, 2021 Zhao Dan, Liu Weida, Chen Ke, Wu Zihan, Yang Huirong, Xu Yanhui. . Structure of the human RNA polymerase I elongation complex Cell Discovery
8eos Oct. 4, 2022 Vishwakarma Rishi K., Qayyum M. Zuhaib, Babitzke Paul, Murakami Katsuhiko S.. . Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase Proceedings of the National Academy of Sciences
8w8p Sept. 4, 2023 Nova Ian C., Craig Jonathan M., Mazumder Abhishek, Laszlo Andrew H., Derrington Ian M., Noakes Matthew T., Brinkerhoff Henry, Yang Shuya, Vahedian-Movahed Hanif, Li Lingting, Zhang Yu, Bowman Jasmine L., Huang Jesse R., Mount Jonathan W., Ebright Richard H., Gundlach Jens H.. . Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase Proceedings of the National Academy of Sciences
9n5c Feb. 4, 2025 Oh Juntaek, Konovalov Kirill A., Hou Peini, Chong Jenny, Huang Xuhui, Wang Dong. . Transcription-Coupled Template Reconfiguration of 8-Oxoguanine for Error-Prone Transcription Revealed by Time-Resolved X-ray Crystallography and Molecular Dynamics Journal of the American Chemical Society

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 481.18 g/mol
HBA not available
HBD not available
HBA + HBD
AlogP not available
TPSA not available
RB not available

Radar chart