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Harnessing RIBOnucleic acid - Small molecules Structures

Compound KSG

Identifiers

  • Canonical SMILES: 
    C[C@H]1O[C@H](O[C@@H]2[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H]2O)[C@@H](N)C[C@@H]1NC(=N)C(O)=O
  • IUPAC name: 
    (1S,2R,3S,4R,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-4-{[(Z)-carboxy(imino)methyl]amino}-2,3,4,6-tetradeoxy-alpha-D-arabino-hexopyranoside
  • InChi: 
    InChI=1S/C14H25N3O9/c1-3-5(17-12(16)13(23)24)2-4(15)14(25-3)26-11-9(21)7(19)6(18)8(20)10(11)22/h3-11,14,18-22H,2,15H2,1H3,(H2,16,17)(H,23,24)/t3-,4+,5+,6-,7+,8+,9-,10+,11+,14-/m1/s1
  • InChiKey: 
    PVTHJAPFENJVNC-MHRBZPPQSA-N
  • SMARTS: 
    [#6]-[#6@H]1-[#8]-[#6@H](-[#8]-[#6@@H]2-[#6@@H](-[#8])-[#6@@H](-[#8])-[#6@H](-[#8])-[#6@H](-[#8])-[#6@H]-2-[#8])-[#6@@H](-[#7])-[#6]-[#6@@H]-1-[#7]-[#6](=[#7])-[#6](-[#8])=[#8]

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

PDB Logo KSG

RNA-SM complexes

PDB code Deposition date Reference publication
2hhh June 28, 2006 Schluenzen Frank, Takemoto Chie, Wilson Daniel N, Kaminishi Tatsuya, Harms Joerg M, Hanawa-Suetsugu Kyoko, Szaflarski Witold, Kawazoe Masahito, Shirouzu Mikako, Nierhaus Knud H, Yokoyama Shigeyuki, Fucini Paola. 2006. The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation Nature Structural & Molecular Biology
2hhh June 28, 2006 Schluenzen Frank, Takemoto Chie, Wilson Daniel N, Kaminishi Tatsuya, Harms Joerg M, Hanawa-Suetsugu Kyoko, Szaflarski Witold, Kawazoe Masahito, Shirouzu Mikako, Nierhaus Knud H, Yokoyama Shigeyuki, Fucini Paola. 2006. The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation Nature Structural & Molecular Biology
4v4h Aug. 4, 2006 Schuwirth Barbara S, Day J Michael, Hau Cathy W, Janssen Gary R, Dahlberg Albert E, Cate Jamie H Doudna, Vila-Sanjurjo Antón. 2006. Structural analysis of kasugamycin inhibition of translation Nature Structural & Molecular Biology
4v4h Aug. 4, 2006 Schuwirth Barbara S, Day J Michael, Hau Cathy W, Janssen Gary R, Dahlberg Albert E, Cate Jamie H Doudna, Vila-Sanjurjo Antón. 2006. Structural analysis of kasugamycin inhibition of translation Nature Structural & Molecular Biology
8cep Feb. 2, 2023 Paternoga Helge, Crowe-McAuliffe Caillan, Bock Lars V., Koller Timm O., Morici Martino, Beckert Bertrand, Myasnikov Alexander G., Grubmüller Helmut, Nováček Jiří, Wilson Daniel N.. 2023. Structural conservation of antibiotic interaction with ribosomes Nature Structural & Molecular Biology
9fco May 15, 2024 Safdari Haaris A., Morici Martino, Sanchez-Castro Ana, Dallapè Andrea, Paternoga Helge, Giuliodori Anna Maria, Fabbretti Attilio, Milón Pohl, Wilson Daniel N.. 2025. The translation inhibitors kasugamycin, edeine and GE81112 target distinct steps during 30S initiation complex formation Nature Communications

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 379.16 g/mol
HBA 10
HBD 9
HBA + HBD
AlogP -4.33
TPSA 218.81
RB 3

Radar chart