HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound 3HE

Identifiers

  • Canonical SMILES: 
    C[C@H]1C[C@H](C)C(=O)[C@@H](C1)[C@H](O)CC2CC(=O)NC(=O)C2
  • IUPAC name: 
    4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione
  • InChi: 
    InChI=1S/C15H23NO4/c1-8-3-9(2)15(20)11(4-8)12(17)5-10-6-13(18)16-14(19)7-10/h8-12,17H,3-7H2,1-2H3,(H,16,18,19)/t8-,9-,11-,12+/m0/s1
  • InChiKey: 
    YPHMISFOHDHNIV-FSZOTQKASA-N
  • SMARTS: 
    [#6]-[#6@H]1-[#6]-[#6@H](-[#6])-[#6](=[#8])-[#6@@H](-[#6]-1)-[#6@H](-[#8])-[#6]-[#6]1-[#6]-[#6](=[#8])-[#7]-[#6](=[#8])-[#6]-1

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

6197 CHEMBL123292 DB20401

RNA-SM complexes

PDB code Deposition date Reference publication
4u3u July 22, 2014 Garreau de Loubresse Nicolas, Prokhorova Irina, Holtkamp Wolf, Rodnina Marina V., Yusupova Gulnara, Yusupov Marat. . Structural basis for the inhibition of the eukaryotic ribosome Nature
4u3u July 22, 2014 Garreau de Loubresse Nicolas, Prokhorova Irina, Holtkamp Wolf, Rodnina Marina V., Yusupova Gulnara, Yusupov Marat. . Structural basis for the inhibition of the eukaryotic ribosome Nature
5gak Dec. 9, 2015 Schmidt Christian, Becker Thomas, Heuer André, Braunger Katharina, Shanmuganathan Vivekanandan, Pech Markus, Berninghausen Otto, Wilson Daniel N., Beckmann Roland. . Structure of the hypusinylated eukaryotic translation factor eIF-5A bound to the ribosome Nucleic Acids Research
5lks July 23, 2016 Myasnikov Alexander G., Kundhavai Natchiar S., Nebout Marielle, Hazemann Isabelle, Imbert Véronique, Khatter Heena, Peyron Jean-François, Klaholz Bruno P.. . Structure–function insights reveal the human ribosome as a cancer target for antibiotics Nature Communications
6hd7 Aug. 17, 2018 Knorr Alexandra G., Schmidt Christian, Tesina Petr, Berninghausen Otto, Becker Thomas, Beatrix Birgitta, Beckmann Roland. . Ribosome–NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation Nature Structural & Molecular Biology
6tnu Dec. 10, 2019 Buschauer Robert, Matsuo Yoshitaka, Sugiyama Takato, Chen Ying-Hsin, Alhusaini Najwa, Sweet Thomas, Ikeuchi Ken, Cheng Jingdong, Matsuki Yasuko, Nobuta Risa, Gilmozzi Andrea, Berninghausen Otto, Tesina Petr, Becker Thomas, Coller Jeff, Inada Toshifumi, Beckmann Roland. . The Ccr4-Not complex monitors the translating ribosome for codon optimality Science
6y0g Feb. 7, 2020 Bhaskar Varun, Graff-Meyer Alexandra, Schenk Andreas D., Cavadini Simone, von Loeffelholz Ottilie, Natchiar S. Kundhavai, Artus-Revel Caroline G., Hotz Hans-Rudolf, Bretones Gabriel, Klaholz Bruno P., Chao Jeffrey A.. . Dynamics of uS19 C-Terminal Tail during the Translation Elongation Cycle in Human Ribosomes Cell Reports
6y2l Feb. 16, 2020 Bhaskar Varun, Graff-Meyer Alexandra, Schenk Andreas D., Cavadini Simone, von Loeffelholz Ottilie, Natchiar S. Kundhavai, Artus-Revel Caroline G., Hotz Hans-Rudolf, Bretones Gabriel, Klaholz Bruno P., Chao Jeffrey A.. . Dynamics of uS19 C-Terminal Tail during the Translation Elongation Cycle in Human Ribosomes Cell Reports
7n8b June 14, 2021 Zhao Yu, Rai Jay, Yu Hongguo, Li Hong. . CryoEM structures of pseudouridine-free ribosome suggest impacts of chemical modifications on ribosome conformations Structure
7q08 Oct. 14, 2021 Zgadzay Yury, Kolosova Olga, Stetsenko Artem, Wu Cheng, Bruchlen David, Usachev Konstantin, Validov Shamil, Jenner Lasse, Rogachev Andrey, Yusupova Gulnara, Sachs Matthew S., Guskov Albert, Yusupov Marat. . E-site drug specificity of the human pathogen Candida albicans ribosome Science Advances
7r81 June 25, 2021 Shen Lunda, Su Zhaoming, Yang Kailu, Wu Cheng, Becker Thomas, Bell-Pedersen Deborah, Zhang Junjie, Sachs Matthew S.. . Structure of the translating Neurospora ribosome arrested by cycloheximide Proceedings of the National Academy of Sciences
8bn3 Nov. 12, 2022 Rauscher Robert, Eggers Cristian, Dimitrova-Paternoga Lyudmila, Shankar Vaishnavi, Rosina Alessia, Cristodero Marina, Paternoga Helge, Wilson Daniel N, Leidel Sebastian A, Polacek Norbert. . Evolving precision: rRNA expansion segment 7S modulates translation velocity and accuracy in eukaryal ribosomes Nucleic Acids Research
8g6j Feb. 15, 2023 Holm Mikael, Natchiar S. Kundhavai, Rundlet Emily J., Myasnikov Alexander G., Watson Zoe L., Altman Roger B., Wang Hao-Yuan, Taunton Jack, Blanchard Scott C.. . mRNA decoding in human is kinetically and structurally distinct from bacteria Nature
8ipa March 14, 2023 Tanaka Mayuki, Yokoyama Takeshi, Saito Hironori, Nishimoto Madoka, Tsuda Kengo, Sotta Naoyuki, Shigematsu Hideki, Shirouzu Mikako, Iwasaki Shintaro, Ito Takuhiro, Fujiwara Toru. . Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1 Nature Chemical Biology
8ipb March 14, 2023 Tanaka Mayuki, Yokoyama Takeshi, Saito Hironori, Nishimoto Madoka, Tsuda Kengo, Sotta Naoyuki, Shigematsu Hideki, Shirouzu Mikako, Iwasaki Shintaro, Ito Takuhiro, Fujiwara Toru. . Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1 Nature Chemical Biology
8t2x June 7, 2023
8t2y June 7, 2023
8t2z June 7, 2023
8t30 June 7, 2023
8ut0 Oct. 30, 2023 Musalgaonkar Sharmishtha, Yelland James N., Chitale Ruta, Rao Shilpa, Ozadam Hakan, Taylor David W., Cenik Can, Johnson Arlen W.. . The assembly factor Reh1 is released from the ribosome during its initial round of translation Nature Communications
8uti Oct. 31, 2023 Musalgaonkar Sharmishtha, Yelland James N., Chitale Ruta, Rao Shilpa, Ozadam Hakan, Taylor David W., Cenik Can, Johnson Arlen W.. . The assembly factor Reh1 is released from the ribosome during its initial round of translation Nature Communications
9bh5 April 19, 2024 Sehgal Enisha, Wohlenberg Chloe, Soukup Evan M., Viscardi Marcus J., Serrão Vitor Hugo Balasco, Arribere Joshua A.. . High-resolution reconstruction of aC. elegansribosome sheds light on evolutionary dynamics and tissue specificity RNA
9cai June 17, 2024 Sehgal Enisha, Wohlenberg Chloe, Soukup Evan M., Viscardi Marcus J., Serrão Vitor Hugo Balasco, Arribere Joshua A.. . High-resolution reconstruction of aC. elegansribosome sheds light on evolutionary dynamics and tissue specificity RNA
9fqz June 17, 2024
9p7h June 20, 2025 Zheng Wei, Zhang Yuekang, Wang Jimin, Wang Shuhui, Chai Pengxin, Bailey Elizabeth J., Zhu Chenghao, Guo Wangbiao, Devarkar Swapnil C., Wu Shenping, Lin Jianfeng, Zhang Kai, Liu Jun, Lomakin Ivan B., Xiong Yong. . Visualizing the translation landscape in human cells at high resolution Nature Communications
9p7i June 20, 2025 Zheng Wei, Zhang Yuekang, Wang Jimin, Wang Shuhui, Chai Pengxin, Bailey Elizabeth J., Zhu Chenghao, Guo Wangbiao, Devarkar Swapnil C., Wu Shenping, Lin Jianfeng, Zhang Kai, Liu Jun, Lomakin Ivan B., Xiong Yong. . Visualizing the translation landscape in human cells at high resolution Nature Communications
9p7j June 20, 2025 Zheng Wei, Zhang Yuekang, Wang Jimin, Wang Shuhui, Chai Pengxin, Bailey Elizabeth J., Zhu Chenghao, Guo Wangbiao, Devarkar Swapnil C., Wu Shenping, Lin Jianfeng, Zhang Kai, Liu Jun, Lomakin Ivan B., Xiong Yong. . Visualizing the translation landscape in human cells at high resolution Nature Communications
9p8i June 23, 2025 Zheng Wei, Zhang Yuekang, Wang Jimin, Wang Shuhui, Chai Pengxin, Bailey Elizabeth J., Zhu Chenghao, Guo Wangbiao, Devarkar Swapnil C., Wu Shenping, Lin Jianfeng, Zhang Kai, Liu Jun, Lomakin Ivan B., Xiong Yong. . Visualizing the translation landscape in human cells at high resolution Nature Communications
9pkb July 14, 2025
9pkd July 14, 2025

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 281.16 g/mol
HBA 4
HBD 2
HBA + HBD
AlogP 1.04
TPSA 83.47
RB 3

Radar chart