HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound AM2

Identifiers

  • Canonical SMILES: 
    CN[C@H]1[C@@H](O)[C@H]2O[C@H](O[C@@H]3[C@@H](N)C[C@@H](N)[C@H](O)[C@H]3O)[C@H](N)C[C@@H]2O[C@@H]1O[C@H]4O[C@H](CO)[C@@H](N)[C@H](O)[C@H]4O
  • IUPAC name: 
    (2R,3R,4S,5S,6S)-5-amino-2-{[(2R,3S,4R,4aR,6S,7R,8aS)-7-amino-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl]oxy}-4-hydroxy-3-(methylamino)octahydropyrano[3,2-b]pyran-2-yl]oxy}-6-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (non-preferred name)
  • InChi: 
    InChI=1S/C21H41N5O11/c1-26-11-14(30)18-8(33-20(11)37-21-16(32)13(29)10(25)9(4-27)34-21)3-7(24)19(36-18)35-17-6(23)2-5(22)12(28)15(17)31/h5-21,26-32H,2-4,22-25H2,1H3/t5-,6+,7-,8+,9-,10-,11+,12+,13+,14-,15-,16-,17-,18+,19+,20-,21-/m1/s1
  • InChiKey: 
    XZNUGFQTQHRASN-XQENGBIVSA-N

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

3081545 CHEMBL1230961 DB04626

RNA-SM complexes

PDB code Deposition date Reference publication
1yrj Feb. 3, 2005 Han Qing, Zhao Qiang, Fish Sarah, Simonsen Klaus B., Vourloumis Dionisios, Froelich Jamie M., Wall Daniel, Hermann Thomas. . Molecular Recognition by Glycoside Pseudo Base Pairs and Triples in an Apramycin–RNA Complex Angewandte Chemie International Edition
1yrj Feb. 3, 2005 Han Qing, Zhao Qiang, Fish Sarah, Simonsen Klaus B., Vourloumis Dionisios, Froelich Jamie M., Wall Daniel, Hermann Thomas. . Molecular Recognition by Glycoside Pseudo Base Pairs and Triples in an Apramycin–RNA Complex Angewandte Chemie International Edition
2g5k Feb. 23, 2006 Kondo Jiro, François Boris, Urzhumtsev Alexandre, Westhof Eric. . Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site Complexed with Apramycin Angewandte Chemie International Edition
2g5k Feb. 23, 2006 Kondo Jiro, François Boris, Urzhumtsev Alexandre, Westhof Eric. . Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site Complexed with Apramycin Angewandte Chemie International Edition
2m4q Feb. 10, 2013 Tsai Albert, Uemura Sotaro, Johansson Magnus, Puglisi Elisabetta Viani, Marshall R. Andrew, Aitken Colin Echeverría, Korlach Jonas, Ehrenberg Måns, Puglisi Joseph D.. . The Impact of Aminoglycosides on the Dynamics of Translation Elongation Cell Reports
2oe5 Dec. 28, 2006 Hermann Thomas, Tereshko Valentina, Skripkin Eugene, Patel Dinshaw J.. . Apramycin recognition by the human ribosomal decoding site Blood Cells, Molecules, and Diseases
2oe8 Dec. 28, 2006 Hermann Thomas, Tereshko Valentina, Skripkin Eugene, Patel Dinshaw J.. . Apramycin recognition by the human ribosomal decoding site Blood Cells, Molecules, and Diseases
4aqy April 20, 2012 Matt Tanja, Ng Chyan Leong, Lang Kathrin, Sha Su-Hua, Akbergenov Rashid, Shcherbakov Dmitri, Meyer Martin, Duscha Stefan, Xie Jing, Dubbaka Srinivas R., Perez-Fernandez Déborah, Vasella Andrea, Ramakrishnan V., Schacht Jochen, Böttger Erik C.. . Dissociation of antibacterial activity and aminoglycoside ototoxicity in the 4-monosubstituted 2-deoxystreptamine apramycin Proceedings of the National Academy of Sciences
4aqy April 20, 2012 Matt Tanja, Ng Chyan Leong, Lang Kathrin, Sha Su-Hua, Akbergenov Rashid, Shcherbakov Dmitri, Meyer Martin, Duscha Stefan, Xie Jing, Dubbaka Srinivas R., Perez-Fernandez Déborah, Vasella Andrea, Ramakrishnan V., Schacht Jochen, Böttger Erik C.. . Dissociation of antibacterial activity and aminoglycoside ototoxicity in the 4-monosubstituted 2-deoxystreptamine apramycin Proceedings of the National Academy of Sciences
4aqy April 20, 2012 Matt Tanja, Ng Chyan Leong, Lang Kathrin, Sha Su-Hua, Akbergenov Rashid, Shcherbakov Dmitri, Meyer Martin, Duscha Stefan, Xie Jing, Dubbaka Srinivas R., Perez-Fernandez Déborah, Vasella Andrea, Ramakrishnan V., Schacht Jochen, Böttger Erik C.. . Dissociation of antibacterial activity and aminoglycoside ototoxicity in the 4-monosubstituted 2-deoxystreptamine apramycin Proceedings of the National Academy of Sciences
4k31 April 10, 2013 Shalev Moran, Kondo Jiro, Kopelyanskiy Dmitry, Jaffe Charles L., Adir Noam, Baasov Timor. . Identification of the molecular attributes required for aminoglycoside activity against Leishmania Proceedings of the National Academy of Sciences
4k31 April 10, 2013 Shalev Moran, Kondo Jiro, Kopelyanskiy Dmitry, Jaffe Charles L., Adir Noam, Baasov Timor. . Identification of the molecular attributes required for aminoglycoside activity against Leishmania Proceedings of the National Academy of Sciences
7pjs Aug. 24, 2021 Petrychenko Valentyn, Peng Bee-Zen, de A. P. Schwarzer Ana C., Peske Frank, Rodnina Marina V., Fischer Niels. . Structural mechanism of GTPase-powered ribosome-tRNA movement Nature Communications
7pjs Aug. 24, 2021 Petrychenko Valentyn, Peng Bee-Zen, de A. P. Schwarzer Ana C., Peske Frank, Rodnina Marina V., Fischer Niels. . Structural mechanism of GTPase-powered ribosome-tRNA movement Nature Communications
7pjs Aug. 24, 2021 Petrychenko Valentyn, Peng Bee-Zen, de A. P. Schwarzer Ana C., Peske Frank, Rodnina Marina V., Fischer Niels. . Structural mechanism of GTPase-powered ribosome-tRNA movement Nature Communications
7pjv Aug. 24, 2021 Petrychenko Valentyn, Peng Bee-Zen, de A. P. Schwarzer Ana C., Peske Frank, Rodnina Marina V., Fischer Niels. . Structural mechanism of GTPase-powered ribosome-tRNA movement Nature Communications
7pjy Aug. 24, 2021 Petrychenko Valentyn, Peng Bee-Zen, de A. P. Schwarzer Ana C., Peske Frank, Rodnina Marina V., Fischer Niels. . Structural mechanism of GTPase-powered ribosome-tRNA movement Nature Communications
7pjy Aug. 24, 2021 Petrychenko Valentyn, Peng Bee-Zen, de A. P. Schwarzer Ana C., Peske Frank, Rodnina Marina V., Fischer Niels. . Structural mechanism of GTPase-powered ribosome-tRNA movement Nature Communications
8cgr Feb. 6, 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.. . Structural conservation of antibiotic interaction with ribosomes Nature Structural & Molecular Biology
8cgr Feb. 6, 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.. . Structural conservation of antibiotic interaction with ribosomes Nature Structural & Molecular Biology
8cgr Feb. 6, 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.. . Structural conservation of antibiotic interaction with ribosomes Nature Structural & Molecular Biology

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 539.28 g/mol
HBA 16
HBD 11
HBA + HBD
AlogP -6.95
TPSA 283.64
RB 6

Radar chart