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Harnessing RIBOnucleic acid - Small molecules Structures

Compound DI0

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@@H]4N[C@@H](COCCOC)O[C@H]([C@H]4C)[C@]1(C)O
  • IUPAC name: 
    (1R,2R,3R,6R,7S,8S,9R,10R,12R,13S,15R,17S)-3-ethyl-2,10-dihydroxy-15-[(2-methoxyethoxy)methyl]-2,6,8,10,12,17-hexamethyl-5-oxo-9-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}-4,16-dioxa-14-azabicyclo[11.3.1]heptadecan-7-yl 2,6-dideoxy-3-C-methyl-3-O-methyl-alpha-L-ribo-hexopyranoside
  • InChi: 
    InChI=1S/C42H78N2O14/c1-15-29-42(10,49)37-24(4)32(43-30(56-37)21-52-17-16-50-13)22(2)19-40(8,48)36(58-39-33(45)28(44(11)12)18-23(3)53-39)25(5)34(26(6)38(47)55-29)57-31-20-41(9,51-14)35(46)27(7)54-31/h22-37,39,43,45-46,48-49H,15-21H2,1-14H3/t22-,23-,24+,25+,26-,27+,28+,29-,30-,31+,32+,33-,34+,35+,36-,37-,39+,40-,41-,42-/m1/s1
  • InChiKey: 
    WLOHNSSYAXHWNR-DWIOZXRMSA-N
  • SMARTS: 
    [#6]-[#6]-[#6@H]1-[#8]-[#6](=[#8])-[#6@H](-[#6])-[#6@@H](-[#8]-[#6@H]2-[#6]-[#6@@](-[#6])(-[#8]-[#6])-[#6@@H](-[#8])-[#6@H](-[#6])-[#8]-2)-[#6@H](-[#6])-[#6@@H](-[#8]-[#6@@H]2-[#8]-[#6@H](-[#6])-[#6]-[#6@@H](-[#6@H]-2-[#8])-[#7](-[#6])-[#6])-[#6@](-[#6])(-[#8])-[#6]-[#6@@H](-[#6])-[#6@@H]2-[#7]-[#6@@H](-[#6]-[#8]-[#6]-[#6]-[#8]-[#6])-[#8]-[#6@H](-[#6@H]-2-[#6])-[#6@]-1(-[#6])-[#8]

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

PubChem Logo 6473883 ChEMBL Logo CHEMBL1237072 PDB Logo DI0 DrugBank Logo DB00954

RNA-SM complexes

PDB code Deposition date Reference publication
6of1 March 28, 2019 Khabibullina Nelli F., Tereshchenkov Andrey G., Komarova Ekaterina S., Syroegin Egor A., Shiriaev Dmitrii I., Paleskava Alena, Kartsev Victor G., Bogdanov Alexey A., Konevega Andrey L., Dontsova Olga A., Sergiev Petr V., Osterman Ilya A., Polikanov Yury S.. 2019. Structure of Dirithromycin Bound to the Bacterial Ribosome Suggests New Ways for Rational Improvement of Macrolides Antimicrobial Agents and Chemotherapy
6of1 March 28, 2019 Khabibullina Nelli F., Tereshchenkov Andrey G., Komarova Ekaterina S., Syroegin Egor A., Shiriaev Dmitrii I., Paleskava Alena, Kartsev Victor G., Bogdanov Alexey A., Konevega Andrey L., Dontsova Olga A., Sergiev Petr V., Osterman Ilya A., Polikanov Yury S.. 2019. Structure of Dirithromycin Bound to the Bacterial Ribosome Suggests New Ways for Rational Improvement of Macrolides Antimicrobial Agents and Chemotherapy
6xz7 Feb. 3, 2020 Pichkur Evgeny B., Paleskava Alena, Tereshchenkov Andrey G., Kasatsky Pavel, Komarova Ekaterina S., Shiriaev Dmitrii I., Bogdanov Alexey A., Dontsova Olga A., Osterman Ilya A., Sergiev Petr V., Polikanov Yury S., Myasnikov Alexander G., Konevega Andrey L.. 2020. Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the E. coli 70S ribosome RNA
6xza Feb. 3, 2020 Pichkur Evgeny B., Paleskava Alena, Tereshchenkov Andrey G., Kasatsky Pavel, Komarova Ekaterina S., Shiriaev Dmitrii I., Bogdanov Alexey A., Dontsova Olga A., Osterman Ilya A., Sergiev Petr V., Polikanov Yury S., Myasnikov Alexander G., Konevega Andrey L.. 2020. Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the E. coli 70S ribosome RNA
6xzb Feb. 3, 2020 Pichkur Evgeny B., Paleskava Alena, Tereshchenkov Andrey G., Kasatsky Pavel, Komarova Ekaterina S., Shiriaev Dmitrii I., Bogdanov Alexey A., Dontsova Olga A., Osterman Ilya A., Sergiev Petr V., Polikanov Yury S., Myasnikov Alexander G., Konevega Andrey L.. 2020. Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the E. coli 70S ribosome RNA

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 834.55 g/mol
HBA 16
HBD 5
HBA + HBD
AlogP 2.20
TPSA 196.33
RB 12

Radar chart