HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound CLM

Identifiers

  • Canonical SMILES: 
    OC[C@@H](NC(=O)C(Cl)Cl)[C@H](O)c1ccc(cc1)[N+]([O-])=O
  • IUPAC name: 
    2,2-dichloro-N-[(1R,2R)-2-hydroxy-1-(hydroxymethyl)-2-(4-nitrophenyl)ethyl]acetamide
  • InChi: 
    InChI=1S/C11H12Cl2N2O5/c12-10(13)11(18)14-8(5-16)9(17)6-1-3-7(4-2-6)15(19)20/h1-4,8-10,16-17H,5H2,(H,14,18)/t8-,9-/m1/s1
  • InChiKey: 
    WIIZWVCIJKGZOK-RKDXNWHRSA-N

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

5959 CHEMBL130 DB00446

RNA-SM complexes

PDB code Deposition date Reference publication
1k01 Sept. 17, 2001 Schlünzen Frank, Zarivach Raz, Harms Jörg, Bashan Anat, Tocilj Ante, Albrecht Renate, Yonath Ada, Franceschi François. . Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria Nature
1nji Dec. 31, 2002 Hansen Jeffrey L., Moore Peter B., Steitz Thomas A.. . Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit Journal of Molecular Biology
28jw Feb. 4, 2026 Waltz Florent, Lehner Philippe A., Van der Stappen Philippe, Kater Lukas, Pfeffer Stefan, Engel Benjamin D.. . Chloroplast-encoded small subunit extensions reshape the Chlamydomonas chlororibosome []
3jbv Oct. 16, 2015 Zhang Jun, Pan Xijiang, Yan Kaige, Sun Shan, Gao Ning, Sui Sen-Fang. . Mechanisms of ribosome stalling by SecM at multiple elongation steps eLife
4v7t Aug. 14, 2010 Dunkle Jack A., Xiong Liqun, Mankin Alexander S., Cate Jamie H. D.. . Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action Proceedings of the National Academy of Sciences
4v7w Aug. 16, 2010 Bulkley David, Innis C. Axel, Blaha Gregor, Steitz Thomas A.. . Revisiting the structures of several antibiotics bound to the bacterial ribosome Proceedings of the National Academy of Sciences
4v7w Aug. 16, 2010 Bulkley David, Innis C. Axel, Blaha Gregor, Steitz Thomas A.. . Revisiting the structures of several antibiotics bound to the bacterial ribosome Proceedings of the National Academy of Sciences
6nd5 Dec. 13, 2018 Svetlov Maxim S., Plessa Elena, Chen Chih-Wei, Bougas Anthony, Krokidis Marios G., Dinos George P., Polikanov Yury S.. . High-resolution crystal structures of ribosome-bound chloramphenicol and erythromycin provide the ultimate basis for their competition RNA
6nd5 Dec. 13, 2018 Svetlov Maxim S., Plessa Elena, Chen Chih-Wei, Bougas Anthony, Krokidis Marios G., Dinos George P., Polikanov Yury S.. . High-resolution crystal structures of ribosome-bound chloramphenicol and erythromycin provide the ultimate basis for their competition RNA
7ood May 27, 2021 Xue Liang, Lenz Swantje, Zimmermann-Kogadeeva Maria, Tegunov Dimitry, Cramer Patrick, Bork Peer, Rappsilber Juri, Mahamid Julia. . Visualizing translation dynamics at atomic detail inside a bacterial cell Nature
7p3k July 8, 2021 Su Ting, Kudva Renuka, Becker Thomas, Buschauer Robert, Komar Tobias, Berninghausen Otto, von Heijne Gunnar, Cheng Jingdong, Beckmann Roland. . Structural basis of l-tryptophan-dependent inhibition of release factor 2 by the TnaC arrest peptide Nucleic Acids Research
7phb Aug. 16, 2021 Xue Liang, Lenz Swantje, Zimmermann-Kogadeeva Maria, Tegunov Dimitry, Cramer Patrick, Bork Peer, Rappsilber Juri, Mahamid Julia. . Visualizing translation dynamics at atomic detail inside a bacterial cell Nature
7rqd Aug. 6, 2021 Syroegin Egor A., Flemmich Laurin, Klepacki Dorota, Vazquez-Laslop Nora, Micura Ronald, Polikanov Yury S.. . Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol Nature Structural & Molecular Biology
7rqd Aug. 6, 2021 Syroegin Egor A., Flemmich Laurin, Klepacki Dorota, Vazquez-Laslop Nora, Micura Ronald, Polikanov Yury S.. . Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol Nature Structural & Molecular Biology
7rqe Aug. 6, 2021 Syroegin Egor A., Flemmich Laurin, Klepacki Dorota, Vazquez-Laslop Nora, Micura Ronald, Polikanov Yury S.. . Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol Nature Structural & Molecular Biology
7rqe Aug. 6, 2021 Syroegin Egor A., Flemmich Laurin, Klepacki Dorota, Vazquez-Laslop Nora, Micura Ronald, Polikanov Yury S.. . Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol Nature Structural & Molecular Biology
7u2i Feb. 24, 2022 Syroegin Egor A, Aleksandrova Elena V, Polikanov Yury S. . Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine Nucleic Acids Research
7u2i Feb. 24, 2022 Syroegin Egor A, Aleksandrova Elena V, Polikanov Yury S. . Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine Nucleic Acids Research
7u2j Feb. 24, 2022 Syroegin Egor A, Aleksandrova Elena V, Polikanov Yury S. . Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine Nucleic Acids Research
7u2j Feb. 24, 2022 Syroegin Egor A, Aleksandrova Elena V, Polikanov Yury S. . Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine Nucleic Acids Research
8p7x May 31, 2023 Xue Liang, Spahn Christian M. T., Schacherl Magdalena, Mahamid Julia. . Structural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells Nature Structural & Molecular Biology
8p7y May 31, 2023 Xue Liang, Spahn Christian M. T., Schacherl Magdalena, Mahamid Julia. . Structural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells Nature Structural & Molecular Biology
8p8b May 31, 2023 Xue Liang, Spahn Christian M. T., Schacherl Magdalena, Mahamid Julia. . Structural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells Nature Structural & Molecular Biology
8p8v June 2, 2023 Xue Liang, Spahn Christian M. T., Schacherl Magdalena, Mahamid Julia. . Structural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells Nature Structural & Molecular Biology
8p8w June 2, 2023 Xue Liang, Spahn Christian M. T., Schacherl Magdalena, Mahamid Julia. . Structural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells Nature Structural & Molecular Biology
8s1p Feb. 15, 2024 Takada Hiraku, Paternoga Helge, Fujiwara Keigo, Nakamoto Jose A, Park Esther N, Dimitrova-Paternoga Lyudmila, Beckert Bertrand, Saarma Merilin, Tenson Tanel, Buskirk Allen R, Atkinson Gemma C, Chiba Shinobu, Wilson Daniel N, Hauryliuk Vasili. . A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis Nucleic Acids Research
8vr8 Jan. 20, 2024 Majumdar Soneya, Kashyap Amuliya, Koripella Ravi K., Sharma Manjuli R., Hurst-Hess Kelley, Manjari Swati R., Banavali Nilesh K., Ghosh Pallavi, Agrawal Rajendra K.. . HflX-mediated drug resistance through ribosome splitting and rRNA disordering in mycobacteria Proceedings of the National Academy of Sciences
8vrl Jan. 22, 2024 Majumdar Soneya, Kashyap Amuliya, Koripella Ravi K., Sharma Manjuli R., Hurst-Hess Kelley, Manjari Swati R., Banavali Nilesh K., Ghosh Pallavi, Agrawal Rajendra K.. . HflX-mediated drug resistance through ribosome splitting and rRNA disordering in mycobacteria Proceedings of the National Academy of Sciences
9evs April 2, 2024 Skaltsogiannis Vasileios, Wolff Philippe, Nguyen Tan-Trung, Corre Nicolas, Pflieger David, Blevins Todd, Hashem Yaser, Giegé Philippe, Waltz Florent. . Structural insights into cauliflower mitoribosome in translation state and in association with a late assembly factor Nature Communications
9t6h Nov. 7, 2025 Klima Martin, Silhan Jan, Pavlik Pavla, Hercik Kamil, Boura Evzen. . Structure of the hibernating Francisella tularensis ribosome and mechanistic insights into its inhibition by antibiotics Nucleic Acids Research

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 323.13 g/mol
HBA not available
HBD not available
HBA + HBD
AlogP not available
TPSA not available
RB not available

Radar chart