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Harnessing RIBOnucleic acid - Small molecules Structures

Compound A1AED

Identifiers

  • Canonical SMILES: 
    CN1C=C\C(=C/c2sc3ccccc3[n+]2CC(=O)NCc4ccccc4)c5ccccc15
  • IUPAC name: 
    3-[2-(benzylamino)-2-oxoethyl]-2-[(E)-(1-methylquinolin-4(1H)-ylidene)methyl]-1,3-benzothiazol-3-ium
  • InChi: 
    InChI=1S/C27H23N3OS/c1-29-16-15-21(22-11-5-6-12-23(22)29)17-27-30(24-13-7-8-14-25(24)32-27)19-26(31)28-18-20-9-3-2-4-10-20/h2-17H,18-19H2,1H3/p+1
  • InChiKey: 
    ODRPVHJDFXJROA-UHFFFAOYSA-O
  • SMARTS: 
    [#6]-[#7]1-[#6]=[#6]/[#6](=[#6]\[#6]2:[#16]:[#6]3:[#6]:[#6]:[#6]:[#6]:[#6]:3:[#7+]:2-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]2:[#6]:[#6]:[#6]:[#6]:[#6]:2)-[#6]2:[#6]:[#6]:[#6]:[#6]:[#6]:2-1

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

PDB Logo A1AED

RNA-SM complexes

PDB code Deposition date Reference publication
8vxz Feb. 6, 2024 Yang Mo, Prestwood Peri R., Passalacqua Luiz F. M., Balaratnam Sumirtha, Fullenkamp Christopher R., Arney J. Winston, Weeks Kevin M., Ferre-D’Amare Adrian, Schneekloth John S.. 2025. Structure-informed design of an ultrabright RNA-activated fluorophore Nature Chemistry
8vxz Feb. 6, 2024 Yang Mo, Prestwood Peri R., Passalacqua Luiz F. M., Balaratnam Sumirtha, Fullenkamp Christopher R., Arney J. Winston, Weeks Kevin M., Ferre-D’Amare Adrian, Schneekloth John S.. 2025. Structure-informed design of an ultrabright RNA-activated fluorophore Nature Chemistry
8vxz Feb. 6, 2024 Yang Mo, Prestwood Peri R., Passalacqua Luiz F. M., Balaratnam Sumirtha, Fullenkamp Christopher R., Arney J. Winston, Weeks Kevin M., Ferre-D’Amare Adrian, Schneekloth John S.. 2025. Structure-informed design of an ultrabright RNA-activated fluorophore Nature Chemistry

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 438.16 g/mol
HBA 3
HBD 1
HBA + HBD
AlogP 5.01
TPSA 36.22
RB 5

Radar chart