HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound GDP

Identifiers

  • Canonical SMILES: 
    NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  • IUPAC name: 
    guanosine 5'-(trihydrogen diphosphate)
  • InChi: 
    InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
  • InChiKey: 
    QGWNDRXFNXRZMB-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])=[#8])-[#6@@H](-[#8])-[#6@H]-1-[#8]

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

8977 CHEMBL384759 DB04315

RNA-SM complexes

PDB code Deposition date Reference publication
4v5g Sept. 1, 2009 Schmeing T. Martin, Voorhees Rebecca M., Kelley Ann C., Gao Yong-Gui, Murphy Frank V., Weir John R., Ramakrishnan V.. . The Crystal Structure of the Ribosome Bound to EF-Tu and Aminoacyl-tRNA Science
4v5r Dec. 7, 2010 Schmeing T Martin, Voorhees Rebecca M, Kelley Ann C, Ramakrishnan V. . How mutations in tRNA distant from the anticodon affect the fidelity of decoding Nature Structural & Molecular Biology
4v8q Dec. 10, 2011 Neubauer Cajetan, Gillet Reynald, Kelley Ann C., Ramakrishnan V.. . Decoding in the Absence of a Codon by tmRNA and SmpB in the Ribosome Science
4v9l April 24, 2013 Zhou Jie, Lancaster Laura, Donohue John Paul, Noller Harry F.. . Crystal Structures of EF-G–Ribosome Complexes Trapped in Intermediate States of Translocation Science
4wpo Oct. 20, 2014 Lin Jinzhong, Gagnon Matthieu G., Bulkley David, Steitz Thomas A.. . Conformational Changes of Elongation Factor G on the Ribosome during tRNA Translocation Cell
4wqy Oct. 22, 2014 Lin Jinzhong, Gagnon Matthieu G., Bulkley David, Steitz Thomas A.. . Conformational Changes of Elongation Factor G on the Ribosome during tRNA Translocation Cell
4wte Oct. 29, 2014 Appleby Todd C., Perry Jason K., Murakami Eisuke, Barauskas Ona, Feng Joy, Cho Aesop, Fox David, Wetmore Diana R., McGrath Mary E., Ray Adrian S., Sofia Michael J., Swaminathan S., Edwards Thomas E.. . Structural basis for RNA replication by the hepatitis C virus polymerase Science
4wti Oct. 30, 2014 Appleby Todd C., Perry Jason K., Murakami Eisuke, Barauskas Ona, Feng Joy, Cho Aesop, Fox David, Wetmore Diana R., McGrath Mary E., Ray Adrian S., Sofia Michael J., Swaminathan S., Edwards Thomas E.. . Structural basis for RNA replication by the hepatitis C virus polymerase Science
5hau Dec. 30, 2015 Gagnon Matthieu G., Roy Raktim N., Lomakin Ivan B., Florin Tanja, Mankin Alexander S., Steitz Thomas A.. . Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition Nucleic Acids Research
5hau Dec. 30, 2015 Gagnon Matthieu G., Roy Raktim N., Lomakin Ivan B., Florin Tanja, Mankin Alexander S., Steitz Thomas A.. . Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition Nucleic Acids Research
5jup May 10, 2016 Abeyrathne Priyanka D, Koh Cha San, Grant Timothy, Grigorieff Nikolaus, Korostelev Andrei A. . Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome eLife
5juu May 10, 2016 Abeyrathne Priyanka D, Koh Cha San, Grant Timothy, Grigorieff Nikolaus, Korostelev Andrei A. . Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome eLife
5lzs Oct. 2, 2016 Shao Sichen, Murray Jason, Brown Alan, Taunton Jack, Ramakrishnan V., Hegde Ramanujan S.. . Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes Cell
5ot7 Aug. 21, 2017 Macé Kevin, Giudice Emmanuel, Chat Sophie, Gillet Reynald. . The structure of an elongation factor G-ribosome complex captured in the absence of inhibitors Nucleic Acids Research
6gqb June 7, 2018 Pellegrino Simone, Demeshkina Natalia, Mancera-Martinez Eder, Melnikov Sergey, Simonetti Angelita, Myasnikov Alexander, Yusupov Marat, Yusupova Gulnara, Hashem Yaser. . Structural Insights into the Role of Diphthamide on Elongation Factor 2 in mRNA Reading-Frame Maintenance Journal of Molecular Biology
6woo April 25, 2020 Wang Jinfan, Wang Jing, Shin Byung-Sik, Kim Joo-Ran, Dever Thomas E., Puglisi Joseph D., Fernández Israel S.. . Structural basis for the transition from translation initiation to elongation by an 80S-eIF5B complex Nature Communications
7pjv Aug. 24, 2021 Petrychenko Valentyn, Peng Bee-Zen, de A. P. Schwarzer Ana C., Peske Frank, Rodnina Marina V., Fischer Niels. . Structural mechanism of GTPase-powered ribosome-tRNA movement Nature Communications
7pjw Aug. 24, 2021 Petrychenko Valentyn, Peng Bee-Zen, de A. P. Schwarzer Ana C., Peske Frank, Rodnina Marina V., Fischer Niels. . Structural mechanism of GTPase-powered ribosome-tRNA movement Nature Communications
7ssl Nov. 11, 2021 Carbone Christine E., Loveland Anna B., Gamper Howard B., Hou Ya-Ming, Demo Gabriel, Korostelev Andrei A.. . Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP Nature Communications
7st7 Nov. 12, 2021 Carbone Christine E., Loveland Anna B., Gamper Howard B., Hou Ya-Ming, Demo Gabriel, Korostelev Andrei A.. . Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP Nature Communications
7ug6 March 24, 2022 Yelland James N., Bravo Jack P. K., Black Joshua J., Taylor David W., Johnson Arlen W.. . A single 2′-O-methylation of ribosomal RNA gates assembly of a functional ribosome Nature Structural & Molecular Biology
7uqb April 19, 2022 Sekulski Kamil, Cruz Victor Emmanuel, Weirich Christine S., Erzberger Jan P.. . rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly Nature Communications
7uqz April 20, 2022 Sekulski Kamil, Cruz Victor Emmanuel, Weirich Christine S., Erzberger Jan P.. . rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly Nature Communications
7v08 May 10, 2022 Sekulski Kamil, Cruz Victor Emmanuel, Weirich Christine S., Erzberger Jan P.. . rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly Nature Communications
8bsi Nov. 25, 2022 Majumdar Soneya, Emmerich Andrew, Krakovka Sascha, Mandava Chandra Sekhar, Svärd Staffan G, Sanyal Suparna. . Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis Nucleic Acids Research
8evr Oct. 20, 2022 Zhao Yu, Rai Jay, Li Hong. . Regulation of translation by ribosomal RNA pseudouridylation Science Advances
8k2d July 12, 2023 Li Xiang, Wang Mengjiao, Denk Timo, Buschauer Robert, Li Yi, Beckmann Roland, Cheng Jingdong. . Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline Nature Communications
8t3a June 7, 2023
8t3c June 7, 2023
8t3e June 7, 2023
8y5k Jan. 31, 2024
8y5m Jan. 31, 2024
8y5n Jan. 31, 2024
8y5o Jan. 31, 2024
8y5p Jan. 31, 2024
8ydg Feb. 20, 2024
8ydj Feb. 20, 2024
9fqz June 17, 2024
9ghc Aug. 15, 2024 González-López Adrián, Ge Xueliang, Larsson Daniel S. D., Sihlbom Wallem Carina, Sanyal Suparna, Selmer Maria. . Structural mechanism of FusB-mediated rescue from fusidic acid inhibition of protein synthesis Nature Communications
9lju Jan. 15, 2025 Wang De-Ping, Zhao Rong, Hu Wen-Shu, Li Hai-Ning, Cao Ji-Min, Zhou Xin, Xiang Ye. . Structural insights into polymerase-catalyzed FAD capping of hepatitis C virus RNA Nature Communications
9ljw Jan. 15, 2025 Wang De-Ping, Zhao Rong, Hu Wen-Shu, Li Hai-Ning, Cao Ji-Min, Zhou Xin, Xiang Ye. . Structural insights into polymerase-catalyzed FAD capping of hepatitis C virus RNA Nature Communications
9rtu July 3, 2025 Ghosh Dastidar Nilanjan, Freyer Nicola S., Petrychenko Valentyn, de A. P. Schwarzer Ana C., Peng Bee-Zen, Samatova Ekaterina, Kothe Christina, Schmidt Marlen, Peske Frank, Politi Antonio Z., Urlaub Henning, Fischer Niels, Rodnina Marina V., Wohlgemuth Ingo. . Selective silencing of antibiotic-tethered ribosomes as a resistance mechanism against aminoglycosides Nature Communications
9rtv July 3, 2025 Ghosh Dastidar Nilanjan, Freyer Nicola S., Petrychenko Valentyn, de A. P. Schwarzer Ana C., Peng Bee-Zen, Samatova Ekaterina, Kothe Christina, Schmidt Marlen, Peske Frank, Politi Antonio Z., Urlaub Henning, Fischer Niels, Rodnina Marina V., Wohlgemuth Ingo. . Selective silencing of antibiotic-tethered ribosomes as a resistance mechanism against aminoglycosides Nature Communications
9ti8 Dec. 5, 2025
9ti9 Dec. 5, 2025

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 443.02 g/mol
HBA 11
HBD 7
HBA + HBD
AlogP -2.45
TPSA 252.57
RB 6

Radar chart