HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound CTP

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@@H](O)[C@H]2O
  • IUPAC name: 
    cytidine 5'-(tetrahydrogen triphosphate)
  • InChi: 
    InChI=1S/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
  • InChiKey: 
    PCDQPRRSZKQHHS-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]-[#15@@](-[#8])(=[#8])-[#8]-[#15](-[#8])(-[#8])=[#8])-[#6@@H](-[#8])-[#6@H]-1-[#8]

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

6176 CHEMBL223533 DB02431

RNA-SM complexes

PDB code Deposition date Reference publication
1tfy May 27, 2004 Xiong Yong, Steitz Thomas A.. . Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template Nature
1tfy May 27, 2004 Xiong Yong, Steitz Thomas A.. . Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template Nature
2dr8 June 8, 2006 Tomita Kozo, Ishitani Ryuichiro, Fukai Shuya, Nureki Osamu. . Complete crystallographic analysis of the dynamics of CCA sequence addition Nature
2dvi July 31, 2006 Tomita Kozo, Ishitani Ryuichiro, Fukai Shuya, Nureki Osamu. . Complete crystallographic analysis of the dynamics of CCA sequence addition Nature
2zha Feb. 1, 2008 Toh Yukimatsu, Numata Tomoyuki, Watanabe Kazunori, Takeshita Daijiro, Nureki Osamu, Tomita Kozo. . Molecular basis for maintenance of fidelity during the CCA‐adding reaction by a CCA‐adding enzyme The EMBO Journal
3bso Dec. 26, 2007 Zamyatkin Dmitry F., Parra Francisco, Alonso José M. Martín, Harki Daniel A., Peterson Blake R., Grochulski Pawel, Ng Kenneth K.-S.. . Structural Insights into Mechanisms of Catalysis and Inhibition in Norwalk Virus Polymerase Journal of Biological Chemistry
3h5y April 22, 2009 Zamyatkin Dmitry F., Parra Francisco, Machín Ángeles, Grochulski Pawel, Ng Kenneth K.-S.. . Binding of 2′-Amino-2′-Deoxycytidine-5′-Triphosphate to Norovirus Polymerase Induces Rearrangement of the Active Site Journal of Molecular Biology
3jb7 Aug. 3, 2015 Zhang Xing, Ding Ke, Yu Xuekui, Chang Winston, Sun Jingchen, Hong Zhou Z.. . In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus Nature
3ovs Sept. 17, 2010 Pan Baocheng, Xiong Yong, Steitz Thomas A.. . How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA Science
3ovs Sept. 17, 2010 Pan Baocheng, Xiong Yong, Steitz Thomas A.. . How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA Science
3wfr July 23, 2013 Yamashita Seisuke, Takeshita Daijiro, Tomita Kozo. . Translocation and Rotation of tRNA during Template-Independent RNA Polymerization by tRNA Nucleotidyltransferase Structure
3wfr July 23, 2013 Yamashita Seisuke, Takeshita Daijiro, Tomita Kozo. . Translocation and Rotation of tRNA during Template-Independent RNA Polymerization by tRNA Nucleotidyltransferase Structure
3wfr July 23, 2013 Yamashita Seisuke, Takeshita Daijiro, Tomita Kozo. . Translocation and Rotation of tRNA during Template-Independent RNA Polymerization by tRNA Nucleotidyltransferase Structure
3wfr July 23, 2013 Yamashita Seisuke, Takeshita Daijiro, Tomita Kozo. . Translocation and Rotation of tRNA during Template-Independent RNA Polymerization by tRNA Nucleotidyltransferase Structure
4wc7 Sept. 4, 2014 Yamashita Seisuke, Martinez Anna, Tomita Kozo. . Measurement of Acceptor-TΨC Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme Structure
4x4o Dec. 3, 2014 Kuhn Claus-D., Wilusz Jeremy E., Zheng Yuxuan, Beal Peter A., Joshua-Tor Leemor. . On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme Cell
4x4q Dec. 3, 2014 Kuhn Claus-D., Wilusz Jeremy E., Zheng Yuxuan, Beal Peter A., Joshua-Tor Leemor. . On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme Cell
4x4q Dec. 3, 2014 Kuhn Claus-D., Wilusz Jeremy E., Zheng Yuxuan, Beal Peter A., Joshua-Tor Leemor. . On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme Cell
4x4s Dec. 3, 2014 Kuhn Claus-D., Wilusz Jeremy E., Zheng Yuxuan, Beal Peter A., Joshua-Tor Leemor. . On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme Cell
4x4s Dec. 3, 2014 Kuhn Claus-D., Wilusz Jeremy E., Zheng Yuxuan, Beal Peter A., Joshua-Tor Leemor. . On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme Cell
5f8i Dec. 9, 2015 Shu Bo, Gong Peng. . Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation Proceedings of the National Academy of Sciences
6p1u May 20, 2019 Kaminski Andrea M, Chiruvella Kishore K, Ramsden Dale A, Kunkel Thomas A, Bebenek Katarzyna, Pedersen Lars C. . Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2′-guanosine Nucleic Acids Research
6qcv Dec. 31, 2018 Kouba Tomas, Drncová Petra, Cusack Stephen. . Structural snapshots of actively transcribing influenza polymerase Nature Structural & Molecular Biology
6rh3 April 18, 2019 Abdelkareem Mo’men, Saint-André Charlotte, Takacs Maria, Papai Gabor, Crucifix Corinne, Guo Xieyang, Ortiz Julio, Weixlbaumer Albert. . Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation Molecular Cell
6uu1 Oct. 30, 2019 Zuo Yuhong, De Swastik, Feng Yingang, Steitz Thomas A.. . Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation iScience
7uoe April 12, 2022 Malone Brandon F., Perry Jason K., Olinares Paul Dominic B., Lee Hery W., Chen James, Appleby Todd C., Feng Joy Y., Bilello John P., Ng Honkit, Sotiris Johanna, Ebrahim Mark, Chua Eugene Y. D., Mendez Joshua H., Eng Ed T., Landick Robert, Götte Matthias, Chait Brian T., Campbell Elizabeth A., Darst Seth A.. . Structural basis for substrate selection by the SARS-CoV-2 replicase Nature
7w9s Dec. 10, 2021 Li Rui, Wang Meihua, Gong Peng. . Crystal structure of a pre-chemistry viral RNA-dependent RNA polymerase suggests participation of two basic residues in catalysis Nucleic Acids Research
7xd9 March 26, 2022 Wu Jiqin, Wang Xinyu, Liu Qiaojie, Lu Guoliang, Gong Peng. . Structural basis of transition from initiation to elongation in de novo viral RNA-dependent RNA polymerases Proceedings of the National Academy of Sciences
7xd9 March 26, 2022 Wu Jiqin, Wang Xinyu, Liu Qiaojie, Lu Guoliang, Gong Peng. . Structural basis of transition from initiation to elongation in de novo viral RNA-dependent RNA polymerases Proceedings of the National Academy of Sciences
7xd9 March 26, 2022 Wu Jiqin, Wang Xinyu, Liu Qiaojie, Lu Guoliang, Gong Peng. . Structural basis of transition from initiation to elongation in de novo viral RNA-dependent RNA polymerases Proceedings of the National Academy of Sciences
7xd9 March 26, 2022 Wu Jiqin, Wang Xinyu, Liu Qiaojie, Lu Guoliang, Gong Peng. . Structural basis of transition from initiation to elongation in de novo viral RNA-dependent RNA polymerases Proceedings of the National Academy of Sciences
7xd9 March 26, 2022 Wu Jiqin, Wang Xinyu, Liu Qiaojie, Lu Guoliang, Gong Peng. . Structural basis of transition from initiation to elongation in de novo viral RNA-dependent RNA polymerases Proceedings of the National Academy of Sciences
7xd9 March 26, 2022 Wu Jiqin, Wang Xinyu, Liu Qiaojie, Lu Guoliang, Gong Peng. . Structural basis of transition from initiation to elongation in de novo viral RNA-dependent RNA polymerases Proceedings of the National Academy of Sciences
8gzh Sept. 27, 2022 Shen Liqiang, Lai Giorgio, You Linlin, Shi Jing, Wu Xiaoxian, Puiu Maria, Gu Zhanxi, Feng Yu, Yuzenkova Yulia, Zhang Yu. . An SI3-σ arch stabilizes cyanobacteria transcription initiation complex Proceedings of the National Academy of Sciences
8uks Oct. 15, 2023 Gao Shijun, Hou Peini, Oh Juntaek, Wang Dong, Greenberg Marc M.. . Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG Journal of the American Chemical Society
8urw Oct. 26, 2023 Qayyum M. Zuhaib, Imashimizu Masahiko, Leanca Miron, Vishwakarma Rishi K., Riaz-Bradley Amber, Yuzenkova Yulia, Murakami Katsuhiko S.. . Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase Proceedings of the National Academy of Sciences
9f37 April 25, 2024 Drncova Petra, Krischuns Tim, Naffakh Nadia, Cusack Stephen. . High-resolution structure of a replication-initiation like configuration of influenza polymerase active site visualises the essential role of a conserved dibasic motif in the PA subunit []
9ukt April 18, 2025 Duan Wenqian, Kaushik Abhishek, Unarta Ilona C., Wu Yue, Liu Mengjie M. J., Weaver Jacob W., Wang Bing, Rice William J., Luciano Daniel J., Belasco Joel G., Huang Xuhui, Nudler Evgeny, Serganov Alexander. . Molecular basis for noncanonical transcription initiation from Np4A alarmones Nature Chemical Biology
9ymu Oct. 10, 2025 Mueller Andreas U., Darst Seth A.. . Structural basis for multi-subunit DNA-dependent RNA polymerase catalytic activity Molecular Cell

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 482.99 g/mol
HBA 12
HBD 7
HBA + HBD
AlogP -2.21
TPSA 270.42
RB 8

Radar chart