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Harnessing RIBOnucleic acid - Small molecules Structures

Compound W6F

Identifiers

  • Canonical SMILES: 
    CN1C=CC(=C\c2sc3ccccc3[n+]2CC(=O)NCCOCCOCCOCCNC(=O)CCCC[C@@H]4SC[C@@H]5NC(=O)N[C@H]45)/c6ccc(C)cc16
  • IUPAC name: 
    2-[(E)-(1,7-dimethylquinolin-4(1H)-ylidene)methyl]-3-{2,16-dioxo-20-[(3aR,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-6,9,12-trioxa-3,15-diazaicosan-1-yl}-1,3-benzothiazol-3-ium
  • InChi: 
    InChI=1S/C39H50N6O6S2/c1-27-11-12-29-28(13-16-44(2)32(29)23-27)24-37-45(31-7-3-4-8-33(31)53-37)25-36(47)41-15-18-50-20-22-51-21-19-49-17-14-40-35(46)10-6-5-9-34-38-30(26-52-34)42-39(48)43-38/h3-4,7-8,11-13,16,23-24,30,34,38H,5-6,9-10,14-15,17-22,25-26H2,1-2H3,(H3-,40,41,42,43,46,47,48)/p+1/t30-,34-,38?/m0/s1
  • InChiKey: 
    OPDJCBUXWAHTAM-PJXAABHXSA-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]-[#8]-[#6]-[#6]-[#8]-[#6]-[#6]-[#8]-[#6]-[#6]-[#7]-[#6](=[#8])-[#6]-[#6]-[#6]-[#6]-[#6@@H]2-[#16]-[#6]-[#6@@H]3-[#7]-[#6](=[#8])-[#7]-[#6@H]-2-3)-[#6]2:[#6]:[#6]:[#6](-[#6]):[#6]:[#6]:2-1

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

PDB Logo W6F

RNA-SM complexes

PDB code Deposition date Reference publication
8u5j Sept. 12, 2023 Lu Xiaocen, Passalacqua Luiz F M, Nodwell Matthew, Kong Kristen Y S, Caballero-García Guillermo, Dolgosheina Elena V, Ferré-D’Amaré Adrian R, Britton Robert, Unrau Peter J. 2024. Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD Nucleic Acids Research
8u5z Sept. 13, 2023 Lu Xiaocen, Passalacqua Luiz F M, Nodwell Matthew, Kong Kristen Y S, Caballero-García Guillermo, Dolgosheina Elena V, Ferré-D’Amaré Adrian R, Britton Robert, Unrau Peter J. 2024. Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD Nucleic Acids Research
8u5z Sept. 13, 2023 Lu Xiaocen, Passalacqua Luiz F M, Nodwell Matthew, Kong Kristen Y S, Caballero-García Guillermo, Dolgosheina Elena V, Ferré-D’Amaré Adrian R, Britton Robert, Unrau Peter J. 2024. Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD Nucleic Acids Research

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 763.33 g/mol
HBA 9
HBD 4
HBA + HBD
AlogP 4.01
TPSA 134.14
RB 20

Radar chart