HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound GNP

Identifiers

  • Canonical SMILES: 
    NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
  • IUPAC name: 
    5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]guanosine
  • InChi: 
    InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
  • InChiKey: 
    UQABYHGXWYXDTK-UUOKFMHZSA-N
  • SMARTS: 
    [#7]-[#6]1:[#7]:[#6]2:[#7](:[#6]:[#7]:[#6]:2:[#6](=[#8]):[#7]:1)-[#6@@H]1-[#8]-[#6@H](-[#6]-[#8]-[#15@@](-[#8])(=[#8])-[#8]-[#15@@](-[#8])(=[#8])-[#7]-[#15](-[#8])(-[#8])=[#8])-[#6@@H](-[#8])-[#6@H]-1-[#8]

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

135403657 CHEMBL1233085 DB02082

RNA-SM complexes

PDB code Deposition date Reference publication
4ujd June 18, 2014 Yamamoto Hiroshi, Unbehaun Anett, Loerke Justus, Behrmann Elmar, Collier Marianne, Bürger Jörg, Mielke Thorsten, Spahn Christian M T. . Structure of the mammalian 80S initiation complex with initiation factor 5B on HCV-IRES RNA Nature Structural & Molecular Biology
4v85 June 13, 2011 Zhou Jie, Lancaster Laura, Trakhanov Sergei, Noller Harry F.. . Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome RNA
4v89 Nov. 17, 2011 Zhou Jie, Lancaster Laura, Trakhanov Sergei, Noller Harry F.. . Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome RNA
5axn July 31, 2015 Kimura Shoko, Suzuki Tateki, Chen Meirong, Kato Koji, Yu Jian, Nakamura Akiyoshi, Tanaka Isao, Yao Min. . Template-dependent nucleotide addition in the reverse (3′-5′) direction by Thg1-like protein Science Advances
5lzd Sept. 29, 2016 Fischer Niels, Neumann Piotr, Bock Lars V., Maracci Cristina, Wang Zhe, Paleskava Alena, Konevega Andrey L., Schröder Gunnar F, Grubmüller Helmut, Ficner Ralf, Rodnina Marina V., Stark Holger. . The pathway to GTPase activation of elongation factor SelB on the ribosome Nature
5m1j Oct. 7, 2016 Hilal Tarek, Yamamoto Hiroshi, Loerke Justus, Bürger Jörg, Mielke Thorsten, Spahn Christian M.T.. . Structural insights into ribosomal rescue by Dom34 and Hbs1 at near-atomic resolution Nature Communications
5wdt July 6, 2017 Fislage Marcus, Zhang Jingji, Brown Zuben Patrick, Mandava Chandra Sekhar, Sanyal Suparna, Ehrenberg Måns, Frank Joachim. . Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A Nucleic Acids Research
5we4 July 7, 2017 Fislage Marcus, Zhang Jingji, Brown Zuben Patrick, Mandava Chandra Sekhar, Sanyal Suparna, Ehrenberg Måns, Frank Joachim. . Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A Nucleic Acids Research
6ydp March 20, 2020 Kummer Eva, Ban Nenad. . Structural insights into mammalian mitochondrial translation elongation catalyzed by mtEFG1 The EMBO Journal
6ydw March 21, 2020 Kummer Eva, Ban Nenad. . Structural insights into mammalian mitochondrial translation elongation catalyzed by mtEFG1 The EMBO Journal
8gwe Sept. 16, 2022 Yan Liming, Huang Yucen, Ge Ji, Liu Zhenyu, Lu Pengchi, Huang Bo, Gao Shan, Wang Junbo, Tan Liping, Ye Sihan, Yu Fengxi, Lan Weiqi, Xu Shiya, Zhou Feng, Shi Lei, Guddat Luke W., Gao Yan, Rao Zihe, Lou Zhiyong. . A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors Cell
8hl1 Nov. 28, 2022 Wang Ying-Hui, Dai Hong, Zhang Ling, Wu Yun, Wang Jingfen, Wang Chen, Xu Cai-Huang, Hou Hai, Yang Bing, Zhu Yongqun, Zhang Xing, Zhou Jie. . Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome Nucleic Acids Research
9bs0 May 12, 2024 Arpin Dominic, Palacios Armando, Basu Kaustuv, Ortega Joaquin. . The binding of RbgA to a critical 50S assembly intermediate facilitates YphC function in bacterial ribosomal assembly Nucleic Acids Research
9gju Aug. 22, 2024 Sala Fernanda A., Ditter Katja, Dybkov Olexandr, Urlaub Henning, Hillen Hauke S.. . Structural basis of Nipah virus RNA synthesis Nature Communications
9uht April 14, 2025

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 522.01 g/mol
HBA 12
HBD 9
HBA + HBD
AlogP -2.76
TPSA 301.90
RB 8

Radar chart