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Harnessing RIBOnucleic acid - Small molecules Structures

Compound XG4

Identifiers

  • Canonical SMILES: 
    NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
  • IUPAC name: 
    2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine
  • InChi: 
    InChI=1S/C10H17N6O12P3/c11-10-13-8-7(9(18)14-10)12-3-16(8)6-1-4(17)5(27-6)2-26-29(19,20)15-30(21,22)28-31(23,24)25/h3-6,17H,1-2H2,(H2,23,24,25)(H3,11,13,14,18)(H3,15,19,20,21,22)/t4-,5+,6+/m0/s1
  • InChiKey: 
    DWGAAFQEGIMTIA-KVQBGUIXSA-N
  • SMARTS: 
    [#7]-[#6]1:[#7]:[#6]2:[#7](:[#6]:[#7]:[#6]:2:[#6](=[#8]):[#7]:1)-[#6@H]1-[#6]-[#6@H](-[#8])-[#6@@H](-[#6]-[#8]-[#15](-[#8])(=[#8])-[#7]-[#15](-[#8])(=[#8])-[#8]-[#15](-[#8])(-[#8])=[#8])-[#8]-1

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

PubChem Logo 135499669 PDB Logo XG4

RNA-SM complexes

PDB code Deposition date Reference publication
8e85 Aug. 25, 2022 Chang Caleb, Lee Luo Christie, Eleraky Sarah, Lin Aaron, Zhou Grace, Gao Yang. 2023. Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity Journal of Biological Chemistry
8e86 Aug. 25, 2022 Chang Caleb, Lee Luo Christie, Eleraky Sarah, Lin Aaron, Zhou Grace, Gao Yang. 2023. Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity Journal of Biological Chemistry
8e87 Aug. 25, 2022 Chang Caleb, Lee Luo Christie, Eleraky Sarah, Lin Aaron, Zhou Grace, Gao Yang. 2023. Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity Journal of Biological Chemistry
8e88 Aug. 25, 2022 Chang Caleb, Lee Luo Christie, Eleraky Sarah, Lin Aaron, Zhou Grace, Gao Yang. 2023. Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity Journal of Biological Chemistry
8e8j Aug. 25, 2022 Chang Caleb, Lee Luo Christie, Eleraky Sarah, Lin Aaron, Zhou Grace, Gao Yang. 2023. Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity Journal of Biological Chemistry
8e8k Aug. 25, 2022 Chang Caleb, Lee Luo Christie, Eleraky Sarah, Lin Aaron, Zhou Grace, Gao Yang. 2023. Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity Journal of Biological Chemistry
9q16 Aug. 13, 2025 No publication
9q17 Aug. 13, 2025 No publication

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 506.01 g/mol
HBA 11
HBD 8
HBA + HBD
AlogP -1.73
TPSA 281.67
RB 8

Radar chart