HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound ERY

Identifiers

  • Canonical SMILES: 
    CC[C@H]1OC(=O)[C@H](C)[C@@H](O[C@H]2C[C@@](C)(OC)[C@@H](O)[C@H](C)O2)[C@H](C)[C@@H](O[C@@H]3O[C@H](C)C[C@@H]([C@H]3O)N(C)C)[C@](C)(O)C[C@@H](C)C(=O)[C@H](C)[C@@H](O)[C@]1(C)O
  • IUPAC name: 
    (3R,4S,5S,6R,7R,9R,11R,12R,13S,14R)-6-{[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-14-ethyl-7,12,13-trihydroxy-4-{[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyltetrahydro-2H-pyran-2-yl]oxy}-3,5,7,9,11,13-hexamethyloxacyclotetradecane-2,10-dione (non-preferred name)
  • InChi: 
    InChI=1S/C37H67NO13/c1-14-25-37(10,45)30(41)20(4)27(39)18(2)16-35(8,44)32(51-34-28(40)24(38(11)12)15-19(3)47-34)21(5)29(22(6)33(43)49-25)50-26-17-36(9,46-13)31(42)23(7)48-26/h18-26,28-32,34,40-42,44-45H,14-17H2,1-13H3/t18-,19-,20+,21+,22-,23+,24+,25-,26+,28-,29+,30-,31+,32-,34+,35-,36-,37-/m1/s1
  • InChiKey: 
    ULGZDMOVFRHVEP-RWJQBGPGSA-N

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

12560 CHEMBL532 DB00199

RNA-SM complexes

PDB code Deposition date Reference publication
1jzy 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
1yi2 Jan. 11, 2005 Tu Daqi, Blaha Gregor, Moore Peter B., Steitz Thomas A.. . Structures of MLSBK Antibiotics Bound to Mutated Large Ribosomal Subunits Provide a Structural Explanation for Resistance Cell
3j5l Oct. 23, 2013 Arenz Stefan, Ramu Haripriya, Gupta Pulkit, Berninghausen Otto, Beckmann Roland, Vázquez-Laslop Nora, Mankin Alexander S., Wilson Daniel N.. . Molecular basis for erythromycin-dependent ribosome stalling during translation of the ErmBL leader peptide Nature Communications
3j7z Aug. 27, 2014 Arenz Stefan, Meydan Sezen, Starosta Agata L., Berninghausen Otto, Beckmann Roland, Vázquez-Laslop Nora, Wilson Daniel N.. . Drug Sensing by the Ribosome Induces Translational Arrest via Active Site Perturbation Molecular Cell
4v7u Aug. 15, 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
4v7x Aug. 17, 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
4v7x Aug. 17, 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
4wfn Sept. 16, 2014 Wekselman Itai, Zimmerman Ella, Davidovich Chen, Belousoff Matthew, Matzov Donna, Krupkin Miri, Rozenberg Haim, Bashan Anat, Friedlander Gilgi, Kjeldgaard Jette, Ingmer Hanne, Lindahl Lasse, Zengel Janice M., Yonath Ada. . The Ribosomal Protein uL22 Modulates the Shape of the Protein Exit Tunnel Structure
5jte May 9, 2016 Arenz Stefan, Bock Lars V., Graf Michael, Innis C. Axel, Beckmann Roland, Grubmüller Helmut, Vaiana Andrea C., Wilson Daniel N.. . A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest Nature Communications
5ju8 May 10, 2016 Arenz Stefan, Bock Lars V., Graf Michael, Innis C. Axel, Beckmann Roland, Grubmüller Helmut, Vaiana Andrea C., Wilson Daniel N.. . A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest Nature Communications
6nd6 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
6nd6 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
6s0x June 18, 2019 Halfon Yehuda, Matzov Donna, Eyal Zohar, Bashan Anat, Zimmerman Ella, Kjeldgaard Jette, Ingmer Hanne, Yonath Ada. . Exit tunnel modulation as resistance mechanism of S. aureus erythromycin resistant mutant Scientific Reports
6s0z June 18, 2019 Halfon Yehuda, Matzov Donna, Eyal Zohar, Bashan Anat, Zimmerman Ella, Kjeldgaard Jette, Ingmer Hanne, Yonath Ada. . Exit tunnel modulation as resistance mechanism of S. aureus erythromycin resistant mutant Scientific Reports
6xhx June 19, 2020 Svetlov Maxim S., Syroegin Egor A., Aleksandrova Elena V., Atkinson Gemma C., Gregory Steven T., Mankin Alexander S., Polikanov Yury S.. . Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance Nature Chemical Biology
6xhx June 19, 2020 Svetlov Maxim S., Syroegin Egor A., Aleksandrova Elena V., Atkinson Gemma C., Gregory Steven T., Mankin Alexander S., Polikanov Yury S.. . Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance Nature Chemical Biology
7b5k Dec. 3, 2020
7nso March 8, 2021 Beckert Bertrand, Leroy Elodie C., Sothiselvam Shanmugapriya, Bock Lars V., Svetlov Maxim S., Graf Michael, Arenz Stefan, Abdelshahid Maha, Seip Britta, Grubmüller Helmut, Mankin Alexander S., Innis C. Axel, Vázquez-Laslop Nora, Wilson Daniel N.. . Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics Nature Communications
7nsp March 8, 2021 Beckert Bertrand, Leroy Elodie C., Sothiselvam Shanmugapriya, Bock Lars V., Svetlov Maxim S., Graf Michael, Arenz Stefan, Abdelshahid Maha, Seip Britta, Grubmüller Helmut, Mankin Alexander S., Innis C. Axel, Vázquez-Laslop Nora, Wilson Daniel N.. . Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics Nature Communications
7q4k Oct. 31, 2021 Fostier Corentin R., Ousalem Farès, Leroy Elodie C., Ngo Saravuth, Soufari Heddy, Innis C. Axel, Hashem Yaser, Boël Grégory. . Regulation of the macrolide resistance ABC-F translation factor MsrD Nature Communications
8fc1 Dec. 1, 2022 Chen Chih-Wei, Leimer Nadja, Syroegin Egor A., Dunand Clémence, Bulman Zackery P., Lewis Kim, Polikanov Yury S., Svetlov Maxim S.. . Structural insights into the mechanism of overcoming Erm-mediated resistance by macrolides acting together with hygromycin-A Nature Communications
8fc1 Dec. 1, 2022 Chen Chih-Wei, Leimer Nadja, Syroegin Egor A., Dunand Clémence, Bulman Zackery P., Lewis Kim, Polikanov Yury S., Svetlov Maxim S.. . Structural insights into the mechanism of overcoming Erm-mediated resistance by macrolides acting together with hygromycin-A Nature Communications
8fc4 Dec. 1, 2022 Chen Chih-Wei, Leimer Nadja, Syroegin Egor A., Dunand Clémence, Bulman Zackery P., Lewis Kim, Polikanov Yury S., Svetlov Maxim S.. . Structural insights into the mechanism of overcoming Erm-mediated resistance by macrolides acting together with hygromycin-A Nature Communications
8vpk Jan. 16, 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
8vr4 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
8xz3 Jan. 20, 2024 Srinivasan Krishnamoorthi, Banerjee Aneek, Sengupta Jayati. . Cryo-EM structures reveal the molecular mechanism of HflX-mediated erythromycin resistance in mycobacteria Structure
9o3h April 7, 2025 Syroegin Egor A., Aleksandrova Elena V., Kruglov Artem A., Paranjpe Madhura N., Svetlov Maxim S., Polikanov Yury S.. . Structural insights into context-specific inhibition of bacterial translation by macrolides []
9o3h April 7, 2025 Syroegin Egor A., Aleksandrova Elena V., Kruglov Artem A., Paranjpe Madhura N., Svetlov Maxim S., Polikanov Yury S.. . Structural insights into context-specific inhibition of bacterial translation by macrolides []
9o3k April 7, 2025 Syroegin Egor A., Aleksandrova Elena V., Kruglov Artem A., Paranjpe Madhura N., Svetlov Maxim S., Polikanov Yury S.. . Structural insights into context-specific inhibition of bacterial translation by macrolides []
9o3k April 7, 2025 Syroegin Egor A., Aleksandrova Elena V., Kruglov Artem A., Paranjpe Madhura N., Svetlov Maxim S., Polikanov Yury S.. . Structural insights into context-specific inhibition of bacterial translation by macrolides []
9o3l April 7, 2025 Syroegin Egor A., Aleksandrova Elena V., Kruglov Artem A., Paranjpe Madhura N., Svetlov Maxim S., Polikanov Yury S.. . Structural insights into context-specific inhibition of bacterial translation by macrolides []
9o3l April 7, 2025 Syroegin Egor A., Aleksandrova Elena V., Kruglov Artem A., Paranjpe Madhura N., Svetlov Maxim S., Polikanov Yury S.. . Structural insights into context-specific inhibition of bacterial translation by macrolides []

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 733.46 g/mol
HBA 14
HBD 5
HBA + HBD
AlogP 1.79
TPSA 193.91
RB 7

Radar chart