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Harnessing RIBOnucleic acid - Small molecules Structures

Compound T8B

Identifiers

  • Canonical SMILES: 
    COC(=O)C1=Cc2cc3cc4cc(CC(O)=O)c(C(=O)\C=C(/O)c5ccccc5O)c(OC)c4c(OC)c3c(O)c2C(=O)O1
  • IUPAC name: 
    {12-hydroxy-9-[(2Z)-3-hydroxy-3-(2-hydroxyphenyl)prop-2-enoyl]-10,11-dimethoxy-3-(methoxycarbonyl)-1-oxo-1H-naphtho[2,3-g]isochromen-8-yl}acetic acid
  • InChi: 
    InChI=1S/C32H24O12/c1-41-29-24(21(35)13-20(34)18-6-4-5-7-19(18)33)17(12-23(36)37)10-15-8-14-9-16-11-22(31(39)43-3)44-32(40)26(16)28(38)25(14)30(42-2)27(15)29/h4-11,13,33-34,38H,12H2,1-3H3,(H,36,37)/b20-13-
  • InChiKey: 
    GGEDVBUCHDZLTH-MOSHPQCFSA-N
  • SMARTS: 
    [#6]-[#8]-[#6](=[#8])-[#6]1:[#6]:[#6]2:[#6]:[#6]3:[#6]:[#6]4:[#6]:[#6](-[#6]-[#6](-[#8])=[#8]):[#6](-[#6](=[#8])/[#6]=[#6](\[#8])-[#6]5:[#6]:[#6]:[#6]:[#6]:[#6]:5-[#8]):[#6](-[#8]-[#6]):[#6]:4:[#6](-[#8]-[#6]):[#6]:3:[#6](-[#8]):[#6]:2:[#6](=[#8]):[#8]:1

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

PubChem Logo 5458199 ChEMBL Logo CHEMBL2261578 PDB Logo T8B

RNA-SM complexes

PDB code Deposition date Reference publication
4v8a Dec. 5, 2011 Bulkley David, Johnson Francis, Steitz Thomas A.. 2012. The Antibiotic Thermorubin Inhibits Protein Synthesis by Binding to Inter-Subunit Bridge B2a of the Ribosome Journal of Molecular Biology
4v8a Dec. 5, 2011 Bulkley David, Johnson Francis, Steitz Thomas A.. 2012. The Antibiotic Thermorubin Inhibits Protein Synthesis by Binding to Inter-Subunit Bridge B2a of the Ribosome Journal of Molecular Biology
8aye Sept. 2, 2022 Parajuli Narayan Prasad, Emmerich Andrew, Mandava Chandra Sekhar, Pavlov Michael Y., Sanyal Suparna. 2023. Antibiotic thermorubin tethers ribosomal subunits and impedes A-site interactions to perturb protein synthesis in bacteria Nature Communications
8ekc Sept. 20, 2022 Paranjpe Madhura N, Marina Valeria I, Grachev Aleksandr A, Maviza Tinashe P, Tolicheva Olga A, Paleskava Alena, Osterman Ilya A, Sergiev Petr V, Konevega Andrey L, Polikanov Yury S, Gagnon Matthieu G. 2023. Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin Nucleic Acids Research

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 600.13 g/mol
HBA 11
HBD 4
HBA + HBD
AlogP 4.72
TPSA 190.03
RB 8

Radar chart