HARIBOSS logo

HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound GCP

Identifiers

  • Canonical SMILES: 
    NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
  • IUPAC name: 
    5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]guanosine
  • InChi: 
    InChI=1S/C11H18N5O13P3/c12-11-14-8-5(9(19)15-11)13-2-16(8)10-7(18)6(17)4(28-10)1-27-32(25,26)29-31(23,24)3-30(20,21)22/h2,4,6-7,10,17-18H,1,3H2,(H,23,24)(H,25,26)(H2,20,21,22)(H3,12,14,15,19)/t4-,6-,7-,10-/m1/s1
  • InChiKey: 
    PHBDHXOBFUBCJD-KQYNXXCUSA-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])-[#6]-[#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 5280942 PDB Logo GCP DrugBank Logo DB03725

RNA-SM complexes

PDB code Deposition date Reference publication
4v5l Sept. 2, 2010 Voorhees Rebecca M., Schmeing T. Martin, Kelley Ann C., Ramakrishnan V.. 2010. The Mechanism for Activation of GTP Hydrolysis on the Ribosome Science
4v8o July 26, 2011 Jin Hong, Kelley Ann C., Ramakrishnan V.. 2011. Crystal structure of the hybrid state of ribosome in complex with the guanosine triphosphatase release factor 3 Proceedings of the National Academy of Sciences
4v9h March 25, 2013 Tourigny David S., Fernández Israel S., Kelley Ann C., Ramakrishnan V.. 2013. Elongation Factor G Bound to the Ribosome in an Intermediate State of Translocation Science
4v9p May 3, 2013 Pulk Arto, Cate Jamie H. D.. 2013. Control of Ribosomal Subunit Rotation by Elongation Factor G Science
5it7 March 16, 2016 Murray Jason, Savva Christos G, Shin Byung-Sik, Dever Thomas E, Ramakrishnan V, Fernández Israel S. 2016. Structural characterization of ribosome recruitment and translocation by type IV IRES eLife
5j8b April 7, 2016 Gagnon Matthieu G., Lin Jinzhong, Steitz Thomas A.. 2016. Elongation factor 4 remodels the A-site tRNA on the ribosome Proceedings of the National Academy of Sciences
5lzw Oct. 2, 2016 Shao Sichen, Murray Jason, Brown Alan, Taunton Jack, Ramakrishnan V., Hegde Ramanujan S.. 2016. Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes Cell
6gq1 June 7, 2018 Pellegrino Simone, Demeshkina Natalia, Mancera-Martinez Eder, Melnikov Sergey, Simonetti Angelita, Myasnikov Alexander, Yusupov Marat, Yusupova Gulnara, Hashem Yaser. 2018. Structural Insights into the Role of Diphthamide on Elongation Factor 2 in mRNA Reading-Frame Maintenance Journal of Molecular Biology
6gqv June 8, 2018 Pellegrino Simone, Demeshkina Natalia, Mancera-Martinez Eder, Melnikov Sergey, Simonetti Angelita, Myasnikov Alexander, Yusupov Marat, Yusupova Gulnara, Hashem Yaser. 2018. Structural Insights into the Role of Diphthamide on Elongation Factor 2 in mRNA Reading-Frame Maintenance Journal of Molecular Biology
6gxo June 27, 2018 Graf Michael, Huter Paul, Maracci Cristina, Peterek Miroslav, Rodnina Marina V., Wilson Daniel N.. 2018. Visualization of translation termination intermediates trapped by the Apidaecin 137 peptide during RF3-mediated recycling of RF1 Nature Communications
7a5k Aug. 21, 2020 Desai Nirupa, Yang Hanting, Chandrasekaran Viswanathan, Kazi Razina, Minczuk Michal, Ramakrishnan V.. 2020. Elongational stalling activates mitoribosome-associated quality control Science
7k51 Sept. 16, 2020 Demo Gabriel, Gamper Howard B., Loveland Anna B., Masuda Isao, Carbone Christine E., Svidritskiy Egor, Hou Ya-Ming, Korostelev Andrei A.. 2021. Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation Nature Communications
7k55 Sept. 16, 2020 Demo Gabriel, Gamper Howard B., Loveland Anna B., Masuda Isao, Carbone Christine E., Svidritskiy Egor, Hou Ya-Ming, Korostelev Andrei A.. 2021. Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation Nature Communications
7pd3 Aug. 4, 2021 Chandrasekaran Viswanathan, Desai Nirupa, Burton Nicholas O, Yang Hanting, Price Jon, Miska Eric A, Ramakrishnan V. 2021. Visualizing formation of the active site in the mitochondrial ribosome eLife
8fzi Jan. 28, 2023 Li Li, Rybak Mariia Yu., Lin Jinzhong, Gagnon Matthieu G.. 2024. The ribosome termination complex remodels release factor RF3 and ejects GDP Nature Structural & Molecular Biology
8fzj Jan. 28, 2023 Li Li, Rybak Mariia Yu., Lin Jinzhong, Gagnon Matthieu G.. 2024. The ribosome termination complex remodels release factor RF3 and ejects GDP Nature Structural & Molecular Biology
8y5q Jan. 31, 2024 No publication

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 521.01 g/mol
HBA 12
HBD 8
HBA + HBD
AlogP -2.23
TPSA 289.87
RB 8

Radar chart