HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound HYG

Identifiers

  • Canonical SMILES: 
    CN[C@H]1C[C@@H](N)[C@H](O)[C@@H](O[C@@H]2O[C@H](CO)[C@H](O)[C@@H]3O[C@@]4(O[C@@H]([C@@H](N)CO)[C@H](O)[C@@H](O)[C@H]4O)O[C@@H]23)[C@@H]1O
  • IUPAC name: 
    (2R,3'R,3aR,4S,4'R,5'R,6R,6'S,7S,7aS)-4-{[(1R,2S,3R,5S,6R)-3-amino-2,6-dihydroxy-5-(methylamino)cyclohexyl]oxy}-6'-[(1S)-1-amino-2-hydroxyethyl]-6-(hydroxymethyl)octahydro-4H-spiro[1,3-dioxolo[4,5-c]pyran-2,2'-pyran]-3',4',5',7-tetrol (non-preferred name)
  • InChi: 
    InChI=1S/C20H37N3O13/c1-23-7-2-5(21)9(26)15(10(7)27)33-19-17-16(11(28)8(4-25)32-19)35-20(36-17)18(31)13(30)12(29)14(34-20)6(22)3-24/h5-19,23-31H,2-4,21-22H2,1H3/t5-,6+,7+,8-,9+,10-,11+,12-,13-,14+,15-,16+,17-,18-,19+,20-/m1/s1
  • InChiKey: 
    GRRNUXAQVGOGFE-WRWUMOMGSA-N

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

24875318

RNA-SM complexes

PDB code Deposition date Reference publication
1hnz Dec. 8, 2000 Brodersen Ditlev E., Clemons William M., Carter Andrew P., Morgan-Warren Robert J., Wimberly Brian T., Ramakrishnan V.. . The Structural Basis for the Action of the Antibiotics Tetracycline, Pactamycin, and Hygromycin B on the 30S Ribosomal Subunit Cell
4lf5 June 26, 2013
4lfa June 26, 2013
4v64 June 11, 2008 Borovinskaya Maria A., Shoji Shinichiro, Fredrick Kurt, Cate Jamie H.D.. . Structural basis for hygromycin B inhibition of protein biosynthesis RNA
4v64 June 11, 2008 Borovinskaya Maria A., Shoji Shinichiro, Fredrick Kurt, Cate Jamie H.D.. . Structural basis for hygromycin B inhibition of protein biosynthesis RNA
6qzp March 12, 2019 Natchiar S. Kundhavai, Myasnikov Alexander G., Kratzat Hanna, Hazemann Isabelle, Klaholz Bruno P.. . Visualization of chemical modifications in the human 80S ribosome structure Nature
8cqw March 7, 2023 Kolosova Olga, Zgadzay Yury, Stetsenko Artem, Sukhinina Anastasia P., Atamas Anastasia, Validov Shamil, Rogachev Andrey, Usachev Konstantin, Jenner Lasse, Dmitriev Sergey E., Yusupova Gulnara, Guskov Albert, Yusupov Marat. . Mechanism of read-through enhancement by aminoglycosides and mefloquine Proceedings of the National Academy of Sciences
8cqw March 7, 2023 Kolosova Olga, Zgadzay Yury, Stetsenko Artem, Sukhinina Anastasia P., Atamas Anastasia, Validov Shamil, Rogachev Andrey, Usachev Konstantin, Jenner Lasse, Dmitriev Sergey E., Yusupova Gulnara, Guskov Albert, Yusupov Marat. . Mechanism of read-through enhancement by aminoglycosides and mefloquine Proceedings of the National Academy of Sciences
9dov Sept. 19, 2024 Zhao Yu, Xu Chong, Chen Xin, Jin Hong, Li Hong. . Structural basis for hygromycin B inhibition of yeast pseudouridine-deficient ribosomes Science Advances
9dp7 Sept. 20, 2024 Zhao Yu, Xu Chong, Chen Xin, Jin Hong, Li Hong. . Structural basis for hygromycin B inhibition of yeast pseudouridine-deficient ribosomes Science Advances
9fqz June 17, 2024
9i14 Jan. 15, 2025
9ru7 July 3, 2025 Fraticelli Davide, Hiregange Disha Gajanan, Weiss Benjamin, Ogran Ariel, Havkin-Solomon Tal, Roman Irene Martinez, Bashan Anat, Yonath Ada, Dikstein Rivka. . Structural and molecular basis of specialized translation mediated by the ribosome mRNA-binding channel Nature Communications
9ru8 July 3, 2025 Fraticelli Davide, Hiregange Disha Gajanan, Weiss Benjamin, Ogran Ariel, Havkin-Solomon Tal, Roman Irene Martinez, Bashan Anat, Yonath Ada, Dikstein Rivka. . Structural and molecular basis of specialized translation mediated by the ribosome mRNA-binding channel Nature Communications
9ru9 July 3, 2025 Fraticelli Davide, Hiregange Disha Gajanan, Weiss Benjamin, Ogran Ariel, Havkin-Solomon Tal, Roman Irene Martinez, Bashan Anat, Yonath Ada, Dikstein Rivka. . Structural and molecular basis of specialized translation mediated by the ribosome mRNA-binding channel Nature Communications
9ruc July 3, 2025 Fraticelli Davide, Hiregange Disha Gajanan, Weiss Benjamin, Ogran Ariel, Havkin-Solomon Tal, Roman Irene Martinez, Bashan Anat, Yonath Ada, Dikstein Rivka. . Structural and molecular basis of specialized translation mediated by the ribosome mRNA-binding channel Nature Communications
9spf Sept. 17, 2025 Rozman Batsheva, Broennimann Karin, Rajan K. Shanmugha, Nachshon Aharon, Saha Chiranjeet, Arazi Tamar, Mohan Vishnu, Geiger Tamar, Wollner Clayton J., Richner Justin M., Westhof Eric, Yonath Ada, Bashan Anat, Stern-Ginossar Noam. . N1-Methylpseudouridine directly modulates translation dynamics Nature
9spi Sept. 17, 2025 Rozman Batsheva, Broennimann Karin, Rajan K. Shanmugha, Nachshon Aharon, Saha Chiranjeet, Arazi Tamar, Mohan Vishnu, Geiger Tamar, Wollner Clayton J., Richner Justin M., Westhof Eric, Yonath Ada, Bashan Anat, Stern-Ginossar Noam. . N1-Methylpseudouridine directly modulates translation dynamics Nature

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 527.52 g/mol
HBA not available
HBD not available
HBA + HBD
AlogP not available
TPSA not available
RB not available

Radar chart