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Harnessing RIBOnucleic acid - Small molecules Structures

Compound DKM

Identifiers

  • Canonical SMILES: 
    CN(C)[C@H]1CN(C[C@@H]1O)c2c(F)cc3C(=O)C(=C4SC=C5CN(C)c2c3[N@@]45)C(O)=O
  • IUPAC name: 
    5-[(3S,4S)-3-(dimethylamino)-4-hydroxypyrrolidin-1-yl]-6-fluoro-4-methyl-8-oxo-3,4-dihydro-8H-1-thia-4,9b-diazacyclopenta[cd]phenalene-9-carboxylic acid
  • InChi: 
    InChI=1S/C20H21FN4O4S/c1-22(2)12-6-24(7-13(12)26)16-11(21)4-10-15-17(16)23(3)5-9-8-30-19(25(9)15)14(18(10)27)20(28)29/h4,8,12-13,26H,5-7H2,1-3H3,(H,28,29)/t12-,13-/m0/s1
  • InChiKey: 
    JHSMWPKZVMQLKB-STQMWFEESA-N
  • SMARTS: 
    [#6]-[#7](-[#6])-[#6@H]1-[#6]-[#7](-[#6]-[#6@@H]-1-[#8])-[#6]1:[#6](-[#9]):[#6]:[#6]2:[#6](=[#8]):[#6](:[#6]3:[#16]:[#6]:[#6]4-[#6]-[#7](-[#6])-[#6]:1:[#6]:2:[#7]:3:4)-[#6](-[#8])=[#8]

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

PubChem Logo 132275083 PDB Logo DKM

RNA-SM complexes

PDB code Deposition date Reference publication
6bfb Oct. 26, 2017 Rizvi Noreen F., Howe John A., Nahvi Ali, Klein Daniel J., Fischmann Thierry O., Kim Hai-Young, McCoy Mark A., Walker Scott S., Hruza Alan, Richards Matthew P., Chamberlin Chad, Saradjian Peter, Butko Margaret T., Mercado Gabriel, Burchard Julja, Strickland Corey, Dandliker Peter J., Smith Graham F., Nickbarg Elliott B.. 2018. Discovery of Selective RNA-Binding Small Molecules by Affinity-Selection Mass Spectrometry ACS Chemical Biology

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 432.13 g/mol
HBA 7
HBD 2
HBA + HBD
AlogP 1.41
TPSA 88.73
RB 3

Radar chart