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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
  • SMARTS: 
    [#6]-[#16@@+](-[#6]-[#6]-[#6@H](-[#7])-[#6](-[#8-])=[#8])-[#6]-[#6@H]1-[#8]-[#6@H](-[#6@H](-[#8])-[#6@@H]-1-[#8])-[#7]1:[#6]:[#7]:[#6]2:[#6](-[#7]):[#7]:[#6]:[#7]:[#6]:1:2

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

PDB Logo SAM DrugBank Logo DB00118

RNA-SM complexes

PDB code Deposition date Reference publication
21zh Jan. 4, 2026 Hu Qian, Yang Wen, Yu Yunyun, Yi Ran, Zhang Yutong, Duan Leyuan, Li Fudong, Zhang Kaiming, Gong Qingguo, Li Shanshan. 2026. Structure-driven RNA remodeling underlies broad substrate recognition by NSUN2 Science China Life Sciences
22av Jan. 5, 2026 Hu Qian, Yang Wen, Yu Yunyun, Yi Ran, Zhang Yutong, Duan Leyuan, Li Fudong, Zhang Kaiming, Gong Qingguo, Li Shanshan. 2026. Structure-driven RNA remodeling underlies broad substrate recognition by NSUN2 Science China Life Sciences
22ax Jan. 5, 2026 Hu Qian, Yang Wen, Yu Yunyun, Yi Ran, Zhang Yutong, Duan Leyuan, Li Fudong, Zhang Kaiming, Gong Qingguo, Li Shanshan. 2026. Structure-driven RNA remodeling underlies broad substrate recognition by NSUN2 Science China Life Sciences
2gis March 29, 2006 Montange Rebecca K., Batey Robert T.. 2006. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element Nature
2qwy Aug. 10, 2007 Gilbert Sunny D, Rambo Robert P, Van Tyne Daria, Batey Robert T. 2008. Structure of the SAM-II riboswitch bound to S-adenosylmethionine Nature Structural & Molecular Biology
2qwy Aug. 10, 2007 Gilbert Sunny D, Rambo Robert P, Van Tyne Daria, Batey Robert T. 2008. Structure of the SAM-II riboswitch bound to S-adenosylmethionine Nature Structural & Molecular Biology
2qwy Aug. 10, 2007 Gilbert Sunny D, Rambo Robert P, Van Tyne Daria, Batey Robert T. 2008. Structure of the SAM-II riboswitch bound to S-adenosylmethionine Nature Structural & Molecular Biology
2ydh March 21, 2011 Schroeder Kersten T., Daldrop Peter, Lilley David M.J.. 2011. RNA Tertiary Interactions in a Riboswitch Stabilize the Structure of a Kink Turn Structure
2ygh April 17, 2011 Schroeder Kersten T., Daldrop Peter, Lilley David M.J.. 2011. RNA Tertiary Interactions in a Riboswitch Stabilize the Structure of a Kink Turn Structure
3e5c Aug. 13, 2008 Lu Changrui, Smith Angela M, Fuchs Ryan T, Ding Fang, Rajashankar Kanagalaghatta, Henkin Tina M, Ke Ailong. 2008. Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism Nature Structural & Molecular Biology
3gx5 April 1, 2009 Montange Rebecca K., Mondragón Estefanía, van Tyne Daria, Garst Andrew D., Ceres Pablo, Batey Robert T.. 2010. Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch Journal of Molecular Biology
3gx6 April 1, 2009 Montange Rebecca K., Mondragón Estefanía, van Tyne Daria, Garst Andrew D., Ceres Pablo, Batey Robert T.. 2010. Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch Journal of Molecular Biology
3gx7 April 1, 2009 Montange Rebecca K., Mondragón Estefanía, van Tyne Daria, Garst Andrew D., Ceres Pablo, Batey Robert T.. 2010. Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch Journal of Molecular Biology
3iqn Aug. 20, 2009 Stoddard Colby D., Montange Rebecca K., Hennelly Scott P., Rambo Robert P., Sanbonmatsu Karissa Y., Batey Robert T.. 2010. Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain Structure
3iqr Aug. 20, 2009 Stoddard Colby D., Montange Rebecca K., Hennelly Scott P., Rambo Robert P., Sanbonmatsu Karissa Y., Batey Robert T.. 2010. Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain Structure
3v7e Dec. 21, 2011 Baird Nathan J., Zhang Jinwei, Hamma Tomoko, Ferré-D'Amaré Adrian R.. 2012. YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops RNA
3v7e Dec. 21, 2011 Baird Nathan J., Zhang Jinwei, Hamma Tomoko, Ferré-D'Amaré Adrian R.. 2012. YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops RNA
4aob March 25, 2012 Schroeder Kersten T., Daldrop Peter, McPhee Scott A., Lilley David M.J.. 2012. Structure and folding of a rare, natural kink turn in RNA with an A•A pair at the 2b•2n position RNA
4b5r Aug. 7, 2012 Daldrop Peter, Lilley David M.J.. 2013. The plasticity of a structural motif in RNA: Structural polymorphism of a kink turn as a function of its environment RNA
4kqy May 15, 2013 Lu Changrui, Ding Fang, Chowdhury Anirban, Pradhan Vineeta, Tomsic Jerneja, Holmes W. Michael, Henkin Tina M., Ke Ailong. 2010. SAM Recognition and Conformational Switching Mechanism in the Bacillus subtilis yitJ S Box/SAM-I Riboswitch Journal of Molecular Biology
4l81 June 15, 2013 Trausch Jeremiah J., Xu Zhenjiang, Edwards Andrea L., Reyes Francis E., Ross Phillip E., Knight Rob, Batey Robert T.. 2014. Structural basis for diversity in the SAM clan of riboswitches Proceedings of the National Academy of Sciences
4n48 Oct. 8, 2013 Smietanski Miroslaw, Werner Maria, Purta Elzbieta, Kaminska Katarzyna H., Stepinski Janusz, Darzynkiewicz Edward, Nowotny Marcin, Bujnicki Janusz M.. 2014. Structural analysis of human 2′-O-ribose methyltransferases involved in mRNA cap structure formation Nature Communications
4n48 Oct. 8, 2013 Smietanski Miroslaw, Werner Maria, Purta Elzbieta, Kaminska Katarzyna H., Stepinski Janusz, Darzynkiewicz Edward, Nowotny Marcin, Bujnicki Janusz M.. 2014. Structural analysis of human 2′-O-ribose methyltransferases involved in mRNA cap structure formation 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.. 2014. Structural basis for diversity in the SAM clan of riboswitches Proceedings of the National Academy of Sciences
5fjc Oct. 7, 2015 Huang Lin, Wang Jia, Lilley David M. J.. 2016. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
5fk1 Oct. 14, 2015 Huang Lin, Wang Jia, Lilley David M. J.. 2016. 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.. 2016. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
5fk3 Oct. 14, 2015 Huang Lin, Wang Jia, Lilley David M. J.. 2016. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
5fk4 Oct. 14, 2015 Huang Lin, Wang Jia, Lilley David M. J.. 2016. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
5fk5 Oct. 14, 2015 Huang Lin, Wang Jia, Lilley David M. J.. 2016. 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.. 2016. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
5fkd Oct. 15, 2015 Huang Lin, Wang Jia, Lilley David M. J.. 2016. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
5fke Oct. 15, 2015 Huang Lin, Wang Jia, Lilley David M. J.. 2016. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
5fkf Oct. 15, 2015 Huang Lin, Wang Jia, Lilley David M. J.. 2016. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
5fkg Oct. 15, 2015 Huang Lin, Wang Jia, Lilley David M. J.. 2016. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
5fkh Oct. 15, 2015 Huang Lin, Wang Jia, Lilley David M. J.. 2016. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function Nucleic Acids Research
5wws Jan. 4, 2017 Liu Ru-Juan, Long Tao, Li Jing, Li Hao, Wang En-Duo. 2017. Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6 Nucleic Acids Research
5wws Jan. 4, 2017 Liu Ru-Juan, Long Tao, Li Jing, Li Hao, Wang En-Duo. 2017. Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6 Nucleic Acids Research
6aax July 19, 2018 Liu Xiaodan, Shen Shengqi, Wu Pengzhi, Li Fudong, Liu Xing, Wang Chongyuan, Gong Qingguo, Wu Jihui, Yao Xuebiao, Zhang Huafeng, Shi Yunyu. 2019. Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function Nucleic Acids Research
6fz0 March 13, 2018 Huang Lin, Lilley David M J. 2018. Structure and ligand binding of the SAM-V riboswitch Nucleic Acids Research
6las Nov. 13, 2019 Sun Aiai, Gasser Catherina, Li Fudong, Chen Hao, Mair Stefan, Krasheninina Olga, Micura Ronald, Ren Aiming. 2019. SAM-VI riboswitch structure and signature for ligand discrimination Nature Communications
6las Nov. 13, 2019 Sun Aiai, Gasser Catherina, Li Fudong, Chen Hao, Mair Stefan, Krasheninina Olga, Micura Ronald, Ren Aiming. 2019. SAM-VI riboswitch structure and signature for ligand discrimination Nature Communications
6lax Nov. 13, 2019 Sun Aiai, Gasser Catherina, Li Fudong, Chen Hao, Mair Stefan, Krasheninina Olga, Micura Ronald, Ren Aiming. 2019. SAM-VI riboswitch structure and signature for ligand discrimination Nature Communications
6lax Nov. 13, 2019 Sun Aiai, Gasser Catherina, Li Fudong, Chen Hao, Mair Stefan, Krasheninina Olga, Micura Ronald, Ren Aiming. 2019. SAM-VI riboswitch structure and signature for ligand discrimination Nature Communications
6uet Sept. 23, 2019 Zhang Kaiming, Li Shanshan, Kappel Kalli, Pintilie Grigore, Su Zhaoming, Mou Tung-Chung, Schmid Michael F., Das Rhiju, Chiu Wah. 2019. 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. 2020. Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research
6ylb April 7, 2020 Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. 2020. Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research
6ylb April 7, 2020 Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. 2020. Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research
6ylb April 7, 2020 Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. 2020. Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research
6ylb April 7, 2020 Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. 2020. Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research
6ylb April 7, 2020 Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. 2020. Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research
6ylb April 7, 2020 Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. 2020. Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research
6ylb April 7, 2020 Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. 2020. Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research
6ylb April 7, 2020 Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. 2020. Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research
6ymm April 8, 2020 Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. 2020. Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research
6ymm April 8, 2020 Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. 2020. Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research
6ymm April 8, 2020 Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. 2020. Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research
7dwh Jan. 17, 2021 Jiang Hengyi, Gao Yanqing, Zhang Lei, Chen Dongrong, Gan Jianhua, Murchie Alastair I. H.. 2021. The identification and characterization of a selected SAM-dependent methyltransferase ribozyme that is present in natural sequences Nature Catalysis
7dwh Jan. 17, 2021 Jiang Hengyi, Gao Yanqing, Zhang Lei, Chen Dongrong, Gan Jianhua, Murchie Alastair I. H.. 2021. The identification and characterization of a selected SAM-dependent methyltransferase ribozyme that is present in natural sequences Nature Catalysis
7eaf March 7, 2021 Huang Lin, Liao Xinli, Li Mengxiao, Wang Jia, Peng Xuemei, Wilson Timothy J, Lilley David M J. 2021. Structure and folding of four putative kink turns identified in structured RNA species in a test of structural prediction rules Nucleic Acids Research
7jyy Sept. 1, 2020 Minasov George, Rosas-Lemus Monica, Shuvalova Ludmilla, Inniss Nicole L., Brunzelle Joseph S., Daczkowski Courtney M., Hoover Paul, Mesecar Andrew D., Satchell Karla J. F.. 2021. Mn 2+ coordinates Cap-0-RNA to align substrates for efficient 2′- O -methyl transfer by SARS-CoV-2 nsp16 Science Signaling
7jyy Sept. 1, 2020 Minasov George, Rosas-Lemus Monica, Shuvalova Ludmilla, Inniss Nicole L., Brunzelle Joseph S., Daczkowski Courtney M., Hoover Paul, Mesecar Andrew D., Satchell Karla J. F.. 2021. Mn 2+ coordinates Cap-0-RNA to align substrates for efficient 2′- O -methyl transfer by SARS-CoV-2 nsp16 Science Signaling
7mjv April 20, 2021 Esakova Olga A., Grove Tyler L., Yennawar Neela H., Arcinas Arthur J., Wang Bo, Krebs Carsten, Almo Steven C., Booker Squire J.. 2021. Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB Nature
8h0s Sept. 30, 2022 Cho Gyuhyeok, Lee Jangmin, Kim Jungwook. 2023. Identification of a novel 5-aminomethyl-2-thiouridine methyltransferase in tRNA modification Nucleic Acids Research
8h0s Sept. 30, 2022 Cho Gyuhyeok, Lee Jangmin, Kim Jungwook. 2023. Identification of a novel 5-aminomethyl-2-thiouridine methyltransferase in tRNA modification Nucleic Acids Research
8h1b Oct. 1, 2022 Cho Gyuhyeok, Lee Jangmin, Kim Jungwook. 2023. Identification of a novel 5-aminomethyl-2-thiouridine methyltransferase in tRNA modification Nucleic Acids Research
8h1b Oct. 1, 2022 Cho Gyuhyeok, Lee Jangmin, Kim Jungwook. 2023. Identification of a novel 5-aminomethyl-2-thiouridine methyltransferase in tRNA modification Nucleic Acids Research
8p4f May 20, 2023 Garg Gaurika, Dienemann Christian, Farnung Lucas, Schwarz Juliane, Linden Andreas, Urlaub Henning, Cramer Patrick. 2023. Structural insights into human co-transcriptional capping Molecular Cell
8s8w March 7, 2024 Kremling Viviane, Falke Sven, Fernández-García Yaiza, Ehrt Christiane, Kiene Antonia, Klopprogge Bjarne, Scheer Emilie, Barthels Fabian, Middendorf Philipp, Kühn Sebastian, Günther Stephan, Rarey Matthias, Chapman Henry N, Oberthür Dominik, Sprenger Janina. 2024. SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug discovery preprint (eLife)

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 398.14 g/mol
HBA 10
HBD 4
HBA + HBD
AlogP -3.26
TPSA 185.46
RB 7

Radar chart