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Harnessing RIBOnucleic acid - Small molecules Structures

Compound A1A1K

Identifiers

  • Canonical SMILES: 
    CC(C)C[C@@H]1CCO[C@@H]2[C@H](CN[C@@H]2C(=O)N[C@@H]3[C@H](C)\C=C/CC[Se][C@H]4O[C@H]3[C@H](O)[C@H](O)[C@H]4O)C1
  • IUPAC name: 
    (4S,5aS,8S,8aR)-4-(2-methylpropyl)-N-[(1R,5Z,7R,8R,9R,10R,11S,12R)-10,11,12-trihydroxy-7-methyl-13-oxa-2-selenabicyclo[7.3.1]tridec-5-en-8-yl]octahydro-2H-oxepino[2,3-c]pyrrole-8-carboxamide (non-preferred name)
  • InChi: 
    InChI=1S/C25H42N2O6Se/c1-13(2)10-15-7-8-32-22-16(11-15)12-26-18(22)24(31)27-17-14(3)6-4-5-9-34-25-21(30)19(28)20(29)23(17)33-25/h4,6,13-23,25-26,28-30H,5,7-12H2,1-3H3,(H,27,31)/b6-4-/t14-,15+,16+,17-,18+,19+,20-,21-,22-,23-,25-/m1/s1
  • InChiKey: 
    DWSVZZQFMWHDFH-JBYNEVPESA-N
  • SMARTS: 
    [#6]-[#6](-[#6])-[#6]-[#6@@H]1-[#6]-[#6]-[#8]-[#6@@H]2-[#6@H](-[#6]-[#7]-[#6@@H]-2-[#6](=[#8])-[#7]-[#6@@H]2-[#6@H](-[#6])/[#6]=[#6]\[#6]-[#6]-[Se]-[#6@H]3-[#8]-[#6@H]-2-[#6@H](-[#8])-[#6@H](-[#8])-[#6@H]-3-[#8])-[#6]-1

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

PubChem Logo 176508676 PDB Logo A1A1K

RNA-SM complexes

PDB code Deposition date Reference publication
9d0i Aug. 7, 2024 Wu Kelvin J.Y., Aleksandrova Elena V., Robinson Paul J., Benedetto Amy E., Yu Meiyi, Tresco Ben I.C., See Dominic N.Y., Jiang Tong, Ramkissoon Antonio, Dunand Clémence F., Svetlov Maxim S., Lee Joonho, Polikanov Yury S., Myers Andrew G.. 2025. Why sulfur is important in lincosamide antibiotics Chem
9d0i Aug. 7, 2024 Wu Kelvin J.Y., Aleksandrova Elena V., Robinson Paul J., Benedetto Amy E., Yu Meiyi, Tresco Ben I.C., See Dominic N.Y., Jiang Tong, Ramkissoon Antonio, Dunand Clémence F., Svetlov Maxim S., Lee Joonho, Polikanov Yury S., Myers Andrew G.. 2025. Why sulfur is important in lincosamide antibiotics Chem

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 546.22 g/mol
HBA 7
HBD 5
HBA + HBD
AlogP 0.43
TPSA 120.28
RB 4

Radar chart