HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound NMY

Identifiers

  • Canonical SMILES: 
    NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O)[C@H]2O[C@@H]3O[C@H](CO)[C@@H](O[C@H]4O[C@@H](CN)[C@@H](O)[C@H](O)[C@H]4N)[C@H]3O)[C@H](N)[C@@H](O)[C@@H]1O
  • IUPAC name: 
    (1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside
  • InChi: 
    InChI=1S/C23H46N6O13/c24-2-7-13(32)15(34)10(28)21(37-7)40-18-6(27)1-5(26)12(31)20(18)42-23-17(36)19(9(4-30)39-23)41-22-11(29)16(35)14(33)8(3-25)38-22/h5-23,30-36H,1-4,24-29H2/t5-,6+,7-,8+,9-,10-,11-,12+,13-,14-,15-,16-,17-,18-,19-,20-,21-,22-,23+/m1/s1
  • InChiKey: 
    PGBHMTALBVVCIT-VCIWKGPPSA-N

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

8378 CHEMBL184618 DB00452

RNA-SM complexes

PDB code Deposition date Reference publication
4w29 July 2, 2014 Zhou Jie, Lancaster Laura, Donohue John Paul, Noller Harry F.. . How the ribosome hands the A-site tRNA to the P site during EF-G–catalyzed translocation Science
1i9v March 21, 2001 Mikkelsen Nils E., Johansson Kenth, Virtanen Anders, Kirsebom Leif A.. . [] Nature Structural Biology
4v52 June 15, 2007 Borovinskaya Maria A, Pai Raj D, Zhang Wen, Schuwirth Barbara S, Holton James M, Hirokawa Go, Kaji Hideko, Kaji Akira, Cate Jamie H Doudna. . Structural basis for aminoglycoside inhibition of bacterial ribosome recycling Nature Structural & Molecular Biology
2et4 Oct. 27, 2005 Francois B.. . Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding Nucleic Acids Research
4v52 June 15, 2007 Borovinskaya Maria A, Pai Raj D, Zhang Wen, Schuwirth Barbara S, Holton James M, Hirokawa Go, Kaji Hideko, Kaji Akira, Cate Jamie H Doudna. . Structural basis for aminoglycoside inhibition of bacterial ribosome recycling Nature Structural & Molecular Biology
4v9c July 25, 2012 Wang Leyi, Pulk Arto, Wasserman Michael R, Feldman Michael B, Altman Roger B, Cate Jamie H Doudna, Blanchard Scott C. . Allosteric control of the ribosome by small-molecule antibiotics Nature Structural & Molecular Biology
4v52 June 15, 2007 Borovinskaya Maria A, Pai Raj D, Zhang Wen, Schuwirth Barbara S, Holton James M, Hirokawa Go, Kaji Hideko, Kaji Akira, Cate Jamie H Doudna. . Structural basis for aminoglycoside inhibition of bacterial ribosome recycling Nature Structural & Molecular Biology
2a04 June 15, 2005 Zhao Fang, Zhao Qiang, Blount Kenneth F., Han Qing, Tor Yitzhak, Hermann Thomas. . Molecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative Angewandte Chemie International Edition
4v9c July 25, 2012 Wang Leyi, Pulk Arto, Wasserman Michael R, Feldman Michael B, Altman Roger B, Cate Jamie H Doudna, Blanchard Scott C. . Allosteric control of the ribosome by small-molecule antibiotics Nature Structural & Molecular Biology
4lf6 June 26, 2013
4v9c July 25, 2012 Wang Leyi, Pulk Arto, Wasserman Michael R, Feldman Michael B, Altman Roger B, Cate Jamie H Doudna, Blanchard Scott C. . Allosteric control of the ribosome by small-molecule antibiotics Nature Structural & Molecular Biology
4w29 July 2, 2014 Zhou Jie, Lancaster Laura, Donohue John Paul, Noller Harry F.. . How the ribosome hands the A-site tRNA to the P site during EF-G–catalyzed translocation Science
4w29 July 2, 2014 Zhou Jie, Lancaster Laura, Donohue John Paul, Noller Harry F.. . How the ribosome hands the A-site tRNA to the P site during EF-G–catalyzed translocation Science
4v57 July 21, 2007 Borovinskaya Maria A., Shoji Shinichiro, Holton James M., Fredrick Kurt, Cate Jamie H. D.. . A Steric Block in Translation Caused by the Antibiotic Spectinomycin ACS Chemical Biology
4w29 July 2, 2014 Zhou Jie, Lancaster Laura, Donohue John Paul, Noller Harry F.. . How the ribosome hands the A-site tRNA to the P site during EF-G–catalyzed translocation Science
4v57 July 21, 2007 Borovinskaya Maria A., Shoji Shinichiro, Holton James M., Fredrick Kurt, Cate Jamie H. D.. . A Steric Block in Translation Caused by the Antibiotic Spectinomycin ACS Chemical Biology
2a04 June 15, 2005 Zhao Fang, Zhao Qiang, Blount Kenneth F., Han Qing, Tor Yitzhak, Hermann Thomas. . Molecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative Angewandte Chemie International Edition
4v9c July 25, 2012 Wang Leyi, Pulk Arto, Wasserman Michael R, Feldman Michael B, Altman Roger B, Cate Jamie H Doudna, Blanchard Scott C. . Allosteric control of the ribosome by small-molecule antibiotics Nature Structural & Molecular Biology
4w29 July 2, 2014 Zhou Jie, Lancaster Laura, Donohue John Paul, Noller Harry F.. . How the ribosome hands the A-site tRNA to the P site during EF-G–catalyzed translocation Science
4v57 July 21, 2007 Borovinskaya Maria A., Shoji Shinichiro, Holton James M., Fredrick Kurt, Cate Jamie H. D.. . A Steric Block in Translation Caused by the Antibiotic Spectinomycin ACS Chemical Biology
5a9z July 23, 2015 Kumar Veerendra, Chen Yun, Ero Rya, Ahmed Tofayel, Tan Jackie, Li Zhe, Wong Andrew See Weng, Bhushan Shashi, Gao Yong-Gui. . Structure of BipA in GTP form bound to the ratcheted ribosome Proceedings of the National Academy of Sciences
4v57 July 21, 2007 Borovinskaya Maria A., Shoji Shinichiro, Holton James M., Fredrick Kurt, Cate Jamie H. D.. . A Steric Block in Translation Caused by the Antibiotic Spectinomycin ACS Chemical Biology
1ei2 Feb. 23, 2000 Varani L.. . Structural basis for recognition of the RNA major groove in the tau exon 10 splicing regulatory element by aminoglycoside antibiotics Nucleic Acids Research
4lf6 June 26, 2013
5aa0 July 23, 2015 Kumar Veerendra, Chen Yun, Ero Rya, Ahmed Tofayel, Tan Jackie, Li Zhe, Wong Andrew See Weng, Bhushan Shashi, Gao Yong-Gui. . Structure of BipA in GTP form bound to the ratcheted ribosome Proceedings of the National Academy of Sciences
4v9c July 25, 2012 Wang Leyi, Pulk Arto, Wasserman Michael R, Feldman Michael B, Altman Roger B, Cate Jamie H Doudna, Blanchard Scott C. . Allosteric control of the ribosome by small-molecule antibiotics Nature Structural & Molecular Biology
2a04 June 15, 2005 Zhao Fang, Zhao Qiang, Blount Kenneth F., Han Qing, Tor Yitzhak, Hermann Thomas. . Molecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative Angewandte Chemie International Edition
5a9z July 23, 2015 Kumar Veerendra, Chen Yun, Ero Rya, Ahmed Tofayel, Tan Jackie, Li Zhe, Wong Andrew See Weng, Bhushan Shashi, Gao Yong-Gui. . Structure of BipA in GTP form bound to the ratcheted ribosome Proceedings of the National Academy of Sciences
4lfb June 26, 2013
4v52 June 15, 2007 Borovinskaya Maria A, Pai Raj D, Zhang Wen, Schuwirth Barbara S, Holton James M, Hirokawa Go, Kaji Hideko, Kaji Akira, Cate Jamie H Doudna. . Structural basis for aminoglycoside inhibition of bacterial ribosome recycling Nature Structural & Molecular Biology
4v9c July 25, 2012 Wang Leyi, Pulk Arto, Wasserman Michael R, Feldman Michael B, Altman Roger B, Cate Jamie H Doudna, Blanchard Scott C. . Allosteric control of the ribosome by small-molecule antibiotics Nature Structural & Molecular Biology
5aa0 July 23, 2015 Kumar Veerendra, Chen Yun, Ero Rya, Ahmed Tofayel, Tan Jackie, Li Zhe, Wong Andrew See Weng, Bhushan Shashi, Gao Yong-Gui. . Structure of BipA in GTP form bound to the ratcheted ribosome Proceedings of the National Academy of Sciences
4lfb June 26, 2013
2et4 Oct. 27, 2005 Francois B.. . Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding Nucleic Acids Research
2a04 June 15, 2005 Zhao Fang, Zhao Qiang, Blount Kenneth F., Han Qing, Tor Yitzhak, Hermann Thomas. . Molecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative Angewandte Chemie International Edition
4v9c July 25, 2012 Wang Leyi, Pulk Arto, Wasserman Michael R, Feldman Michael B, Altman Roger B, Cate Jamie H Doudna, Blanchard Scott C. . Allosteric control of the ribosome by small-molecule antibiotics Nature Structural & Molecular Biology
4v9c July 25, 2012 Wang Leyi, Pulk Arto, Wasserman Michael R, Feldman Michael B, Altman Roger B, Cate Jamie H Doudna, Blanchard Scott C. . Allosteric control of the ribosome by small-molecule antibiotics Nature Structural & Molecular Biology

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 614.31 g/mol
HBA 19
HBD 13
HBA + HBD
AlogP -8.90
TPSA 353.11
RB 9

Radar chart