HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound SAM

Identifiers

  • Canonical SMILES: 
    C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  • IUPAC name: 
    (2S)-2-amino-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(methyl)sulfonio]butanoate (non-preferred name)
  • InChi: 
    InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
  • InChiKey: 
    MEFKEPWMEQBLKI-FCKMPRQPSA-N

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

RNA-SM complexes

PDB code Deposition date Reference publication
5fkf Oct. 15, 2015 Huang Lin, Wang Jia, Lilley David M. J.. . A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
3gx5 April 1, 2009 Montange Rebecca K., Mondragón Estefanía, van Tyne Daria, Garst Andrew D., Ceres Pablo, Batey Robert T.. . Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch Journal of Molecular Biology
6las Nov. 13, 2019 Sun Aiai, Gasser Catherina, Li Fudong, Chen Hao, Mair Stefan, Krasheninina Olga, Micura Ronald, Ren Aiming. . SAM-VI riboswitch structure and signature for ligand discrimination Nature Communications
6ylb April 7, 2020 Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. . Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research
2ydh March 21, 2011 Schroeder Kersten T., Daldrop Peter, Lilley David M.J.. . RNA Tertiary Interactions in a Riboswitch Stabilize the Structure of a Kink Turn Structure
5fkh Oct. 15, 2015 Huang Lin, Wang Jia, Lilley David M. J.. . A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
2qwy Aug. 10, 2007 Gilbert Sunny D, Rambo Robert P, Van Tyne Daria, Batey Robert T. . Structure of the SAM-II riboswitch bound to S-adenosylmethionine Nature Structural & Molecular Biology
2gis March 29, 2006 Montange Rebecca K., Batey Robert T.. . Structure of the S-adenosylmethionine riboswitch regulatory mRNA element Nature
4b5r Aug. 7, 2012 Daldrop Peter, Lilley David M.J.. . The plasticity of a structural motif in RNA: Structural polymorphism of a kink turn as a function of its environment RNA
5fk1 Oct. 14, 2015 Huang Lin, Wang Jia, Lilley David M. J.. . A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
5fk2 Oct. 14, 2015 Huang Lin, Wang Jia, Lilley David M. J.. . A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
6uet Sept. 23, 2019 Zhang Kaiming, Li Shanshan, Kappel Kalli, Pintilie Grigore, Su Zhaoming, Mou Tung-Chung, Schmid Michael F., Das Rhiju, Chiu Wah. . Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution Nature Communications
6ylb April 7, 2020 Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. . Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research
4l81 June 15, 2013 Trausch Jeremiah J., Xu Zhenjiang, Edwards Andrea L., Reyes Francis E., Ross Phillip E., Knight Rob, Batey Robert T.. . Structural basis for diversity in the SAM clan of riboswitches Proceedings of the National Academy of Sciences
3v7e Dec. 21, 2011 Baird Nathan J., Zhang Jinwei, Hamma Tomoko, Ferré-D'Amaré Adrian R.. . YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops RNA
5fke Oct. 15, 2015 Huang Lin, Wang Jia, Lilley David M. J.. . A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
6lax Nov. 13, 2019 Sun Aiai, Gasser Catherina, Li Fudong, Chen Hao, Mair Stefan, Krasheninina Olga, Micura Ronald, Ren Aiming. . SAM-VI riboswitch structure and signature for ligand discrimination Nature Communications
5fkd Oct. 15, 2015 Huang Lin, Wang Jia, Lilley David M. J.. . A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
6las Nov. 13, 2019 Sun Aiai, Gasser Catherina, Li Fudong, Chen Hao, Mair Stefan, Krasheninina Olga, Micura Ronald, Ren Aiming. . SAM-VI riboswitch structure and signature for ligand discrimination Nature Communications
3e5c Aug. 13, 2008 Lu Changrui, Smith Angela M, Fuchs Ryan T, Ding Fang, Rajashankar Kanagalaghatta, Henkin Tina M, Ke Ailong. . Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism Nature Structural & Molecular Biology
3iqn Aug. 20, 2009 Stoddard Colby D., Montange Rebecca K., Hennelly Scott P., Rambo Robert P., Sanbonmatsu Karissa Y., Batey Robert T.. . Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain Structure
4aob March 25, 2012 Schroeder Kersten T., Daldrop Peter, McPhee Scott A., Lilley David M.J.. . Structure and folding of a rare, natural kink turn in RNA with an A•A pair at the 2b•2n position RNA
2ygh April 17, 2011 Schroeder Kersten T., Daldrop Peter, Lilley David M.J.. . RNA Tertiary Interactions in a Riboswitch Stabilize the Structure of a Kink Turn Structure
2qwy Aug. 10, 2007 Gilbert Sunny D, Rambo Robert P, Van Tyne Daria, Batey Robert T. . Structure of the SAM-II riboswitch bound to S-adenosylmethionine Nature Structural & Molecular Biology
5fkg Oct. 15, 2015 Huang Lin, Wang Jia, Lilley David M. J.. . A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
2qwy Aug. 10, 2007 Gilbert Sunny D, Rambo Robert P, Van Tyne Daria, Batey Robert T. . Structure of the SAM-II riboswitch bound to S-adenosylmethionine Nature Structural & Molecular Biology
3iqr Aug. 20, 2009 Stoddard Colby D., Montange Rebecca K., Hennelly Scott P., Rambo Robert P., Sanbonmatsu Karissa Y., Batey Robert T.. . Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain Structure
3gx7 April 1, 2009 Montange Rebecca K., Mondragón Estefanía, van Tyne Daria, Garst Andrew D., Ceres Pablo, Batey Robert T.. . Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch Journal of Molecular Biology
5fjc Oct. 7, 2015 Huang Lin, Wang Jia, Lilley David M. J.. . A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
7dwh Jan. 17, 2021 Jiang Hengyi, Gao Yanqing, Zhang Lei, Chen Dongrong, Gan Jianhua, Murchie Alastair I. H.. . The identification and characterization of a selected SAM-dependent methyltransferase ribozyme that is present in natural sequences Nature Catalysis
5fk4 Oct. 14, 2015 Huang Lin, Wang Jia, Lilley David M. J.. . A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
3gx6 April 1, 2009 Montange Rebecca K., Mondragón Estefanía, van Tyne Daria, Garst Andrew D., Ceres Pablo, Batey Robert T.. . Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch Journal of Molecular Biology
6lax Nov. 13, 2019 Sun Aiai, Gasser Catherina, Li Fudong, Chen Hao, Mair Stefan, Krasheninina Olga, Micura Ronald, Ren Aiming. . SAM-VI riboswitch structure and signature for ligand discrimination Nature Communications
4oqu Feb. 10, 2014 Trausch Jeremiah J., Xu Zhenjiang, Edwards Andrea L., Reyes Francis E., Ross Phillip E., Knight Rob, Batey Robert T.. . Structural basis for diversity in the SAM clan of riboswitches Proceedings of the National Academy of Sciences
7dwh Jan. 17, 2021 Jiang Hengyi, Gao Yanqing, Zhang Lei, Chen Dongrong, Gan Jianhua, Murchie Alastair I. H.. . The identification and characterization of a selected SAM-dependent methyltransferase ribozyme that is present in natural sequences Nature Catalysis
4kqy May 15, 2013 Lu Changrui, Ding Fang, Chowdhury Anirban, Pradhan Vineeta, Tomsic Jerneja, Holmes W. Michael, Henkin Tina M., Ke Ailong. . SAM Recognition and Conformational Switching Mechanism in the Bacillus subtilis yitJ S Box/SAM-I Riboswitch Journal of Molecular Biology
3v7e Dec. 21, 2011 Baird Nathan J., Zhang Jinwei, Hamma Tomoko, Ferré-D'Amaré Adrian R.. . YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops RNA
6ylb April 7, 2020 Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. . Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research
5fk5 Oct. 14, 2015 Huang Lin, Wang Jia, Lilley David M. J.. . A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
5fk6 Oct. 14, 2015 Huang Lin, Wang Jia, Lilley David M. J.. . A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
6ymm April 8, 2020 Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. . Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research
6fz0 March 13, 2018 Huang Lin, Lilley David M J. . Structure and ligand binding of the SAM-V riboswitch Nucleic Acids Research
5fk3 Oct. 14, 2015 Huang Lin, Wang Jia, Lilley David M. J.. . A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
7eaf March 7, 2021 Huang Lin, Liao Xinli, Li Mengxiao, Wang Jia, Peng Xuemei, Wilson Timothy J, Lilley David M J. . Structure and folding of four putative kink turns identified in structured RNA species in a test of structural prediction rules Nucleic Acids Research

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 398.14 g/mol
HBA 11
HBD 4
HBA + HBD
AlogP -3.26
TPSA 185.46
RB 7

Radar chart