HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound ATP

Identifiers

  • Canonical SMILES: 
    Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  • IUPAC name: 
    adenosine 5'-(tetrahydrogen triphosphate)
  • InChi: 
    InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
  • InChiKey: 
    ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

5957 CHEMBL14249 DB00171

RNA-SM complexes

PDB code Deposition date Reference publication
6nbj Dec. 7, 2018 Stec Boguslaw. . Discovery of the Universal tRNA Binding Mode for the TsaD-like Components of the t6A tRNA Modification Pathway Biophysica
7uo7 April 12, 2022 Malone Brandon F., Perry Jason K., Olinares Paul Dominic B., Lee Hery W., Chen James, Appleby Todd C., Feng Joy Y., Bilello John P., Ng Honkit, Sotiris Johanna, Ebrahim Mark, Chua Eugene Y. D., Mendez Joshua H., Eng Ed T., Landick Robert, Götte Matthias, Chait Brian T., Campbell Elizabeth A., Darst Seth A.. . Structural basis for substrate selection by the SARS-CoV-2 replicase Nature
3vnu Jan. 18, 2012 Takeshita Daijiro, Yamashita Seisuke, Tomita Kozo. . Mechanism for Template-Independent Terminal Adenylation Activity of Qβ Replicase Structure
7n1p May 28, 2021 Rundlet Emily J., Holm Mikael, Schacherl Magdalena, Natchiar S. Kundhavai, Altman Roger B., Spahn Christian M. T., Myasnikov Alexander G., Blanchard Scott C.. . Structural basis of early translocation events on the ribosome Nature
2dxi Aug. 28, 2006 Sekine Shun-ichi, Shichiri Mika, Bernier Stéphane, Chênevert Robert, Lapointe Jacques, Yokoyama Shigeyuki. . Structural Bases of Transfer RNA-Dependent Amino Acid Recognition and Activation by Glutamyl-tRNA Synthetase Structure
7orn June 6, 2021 Arragain Benoît, Durieux Trouilleton Quentin, Baudin Florence, Provaznik Jan, Azevedo Nayara, Cusack Stephen, Schoehn Guy, Malet Hélène. . Structural snapshots of La Crosse virus polymerase reveal the mechanisms underlying Peribunyaviridae replication and transcription Nature Communications
7n30 May 30, 2021 Rundlet Emily J., Holm Mikael, Schacherl Magdalena, Natchiar S. Kundhavai, Altman Roger B., Spahn Christian M. T., Myasnikov Alexander G., Blanchard Scott C.. . Structural basis of early translocation events on the ribosome Nature
7n2v May 29, 2021 Rundlet Emily J., Holm Mikael, Schacherl Magdalena, Natchiar S. Kundhavai, Altman Roger B., Spahn Christian M. T., Myasnikov Alexander G., Blanchard Scott C.. . Structural basis of early translocation events on the ribosome Nature
2cv1 May 31, 2005
3s1q May 16, 2011 Liu Xin, Bushnell David A., Silva Daniel-Adriano, Huang Xuhui, Kornberg Roger D.. . Initiation Complex Structure and Promoter Proofreading Science
9n2c Jan. 28, 2025 Welfer Griffin A., Brady Ryan A., Natchiar S. Kundhavai, Watson Zoe L., Rundlet Emily J., Alejo Jose L., Singh Anand P., Mishra Nitish K., Altman Roger B., Blanchard Scott C.. . Impacts of ribosomal RNA sequence variation on gene expression and phenotype Philosophical Transactions of the Royal Society B: Biological Sciences
6zxh July 29, 2020 Ameismeier Michael, Zemp Ivo, van den Heuvel Jasmin, Thoms Matthias, Berninghausen Otto, Kutay Ulrike, Beckmann Roland. . Structural basis for the final steps of human 40S ribosome maturation Nature
9mn7 Dec. 20, 2024 Herbine Karl, Nayak Ashok R., Zamudio-Ochoa Angelica, Temiakov Dmitry. . Structural basis for promoter recognition and transcription factor binding and release in human mitochondria Molecular Cell
9n2b Jan. 28, 2025 Welfer Griffin A., Brady Ryan A., Natchiar S. Kundhavai, Watson Zoe L., Rundlet Emily J., Alejo Jose L., Singh Anand P., Mishra Nitish K., Altman Roger B., Blanchard Scott C.. . Impacts of ribosomal RNA sequence variation on gene expression and phenotype Philosophical Transactions of the Royal Society B: Biological Sciences
8qyx Oct. 26, 2023 Wiechert Franziska, Unbehaun Anett, Sprink Thiemo, Seibel Helena, Bürger Jörg, Loerke Justus, Mielke Thorsten, Diebolder Christoph A, Schacherl Magdalena, Spahn Christian M T. . Visualizing the modification landscape of the human 60S ribosomal subunit at close to atomic resolution Nucleic Acids Research
6zxf July 29, 2020 Ameismeier Michael, Zemp Ivo, van den Heuvel Jasmin, Thoms Matthias, Berninghausen Otto, Kutay Ulrike, Beckmann Roland. . Structural basis for the final steps of human 40S ribosome maturation Nature
7ork June 6, 2021 Arragain Benoît, Durieux Trouilleton Quentin, Baudin Florence, Provaznik Jan, Azevedo Nayara, Cusack Stephen, Schoehn Guy, Malet Hélène. . Structural snapshots of La Crosse virus polymerase reveal the mechanisms underlying Peribunyaviridae replication and transcription Nature Communications
6tf2 Nov. 12, 2019 Huang Lin, Wang Jia, Lilley David M.J.. . Structure and ligand binding of the ADP-binding domain of the NAD+ riboswitch RNA
8dh5 June 24, 2022 Oh Juntaek, Kimoto Michiko, Xu Haoqing, Chong Jenny, Hirao Ichiro, Wang Dong. . Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase Nature Communications
7n2u May 29, 2021 Rundlet Emily J., Holm Mikael, Schacherl Magdalena, Natchiar S. Kundhavai, Altman Roger B., Spahn Christian M. T., Myasnikov Alexander G., Blanchard Scott C.. . Structural basis of early translocation events on the ribosome Nature
6p1s May 20, 2019 Kaminski Andrea M, Chiruvella Kishore K, Ramsden Dale A, Kunkel Thomas A, Bebenek Katarzyna, Pedersen Lars C. . Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2′-guanosine Nucleic Acids Research
2q66 June 4, 2007 Balbo Paul B., Bohm Andrew. . Mechanism of Poly(A) Polymerase: Structure of the Enzyme-MgATP-RNA Ternary Complex and Kinetic Analysis Structure
7otc June 10, 2021 Wieland Maximiliane, Holm Mikael, Rundlet Emily J., Morici Martino, Koller Timm O., Maviza Tinashe P., Pogorevc Domen, Osterman Ilya A., Müller Rolf, Blanchard Scott C., Wilson Daniel N.. . The cyclic octapeptide antibiotic argyrin B inhibits translation by trapping EF-G on the ribosome during translocation Proceedings of the National Academy of Sciences
7d7y Oct. 6, 2020 Chen Hao, Egger Michaela, Xu Xiaochen, Flemmich Laurin, Krasheninina Olga, Sun Aiai, Micura Ronald, Ren Aiming. . Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding Nucleic Acids Research
3ov7 Sept. 15, 2010 Pan Baocheng, Xiong Yong, Steitz Thomas A.. . How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA Science
9mn8 Dec. 20, 2024 Herbine Karl, Nayak Ashok R., Zamudio-Ochoa Angelica, Temiakov Dmitry. . Structural basis for promoter recognition and transcription factor binding and release in human mitochondria Molecular Cell
7n31 May 31, 2021 Rundlet Emily J., Holm Mikael, Schacherl Magdalena, Natchiar S. Kundhavai, Altman Roger B., Spahn Christian M. T., Myasnikov Alexander G., Blanchard Scott C.. . Structural basis of early translocation events on the ribosome Nature
9qeb March 8, 2025 Li Qingrong, Yi Gangshun, Wu Yue, Xu Sophy, Chong Jenny, Huang Xuhui, Zhang Peijun, Wang Dong. . Sub-2 Å cryo-EM structures of transcribing RNA polymerase II reveal critical roles of water molecules in catalysis Molecular Cell
7n1p May 28, 2021 Rundlet Emily J., Holm Mikael, Schacherl Magdalena, Natchiar S. Kundhavai, Altman Roger B., Spahn Christian M. T., Myasnikov Alexander G., Blanchard Scott C.. . Structural basis of early translocation events on the ribosome Nature
1tfw May 27, 2004 Xiong Yong, Steitz Thomas A.. . Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template Nature
1asz Jan. 19, 1995 Cavarelli J., Eriani G., Rees B., Ruff M., Boeglin M., Mitschler A., Martin F., Gangloff J., Thierry J.C., Moras D.. . The active site of yeast aspartyl‐tRNA synthetase: structural and functional aspects of the aminoacylation reaction. The EMBO Journal
7n31 May 31, 2021 Rundlet Emily J., Holm Mikael, Schacherl Magdalena, Natchiar S. Kundhavai, Altman Roger B., Spahn Christian M. T., Myasnikov Alexander G., Blanchard Scott C.. . Structural basis of early translocation events on the ribosome Nature
4wc6 Sept. 4, 2014 Yamashita Seisuke, Martinez Anna, Tomita Kozo. . Measurement of Acceptor-TΨC Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme Structure
3ovb Sept. 16, 2010 Pan Baocheng, Xiong Yong, Steitz Thomas A.. . How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA Science
1qru June 14, 1996 Arnez John G., Steitz Thomas A.. . Crystal Structures of Three Misacylating Mutants of Escherichia coli Glutaminyl-tRNA Synthetase Complexed with tRNAGln and ATP Biochemistry
9n5g Feb. 4, 2025 Oh Juntaek, Konovalov Kirill A., Hou Peini, Chong Jenny, Huang Xuhui, Wang Dong. . Transcription-Coupled Template Reconfiguration of 8-Oxoguanine for Error-Prone Transcription Revealed by Time-Resolved X-ray Crystallography and Molecular Dynamics Journal of the American Chemical Society
2hvy July 31, 2006 Li Ling, Ye Keqiong. . Crystal structure of an H/ACA box ribonucleoprotein particle Nature
1tfw May 27, 2004 Xiong Yong, Steitz Thomas A.. . Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template Nature
9mna Dec. 20, 2024 Herbine Karl, Nayak Ashok R., Zamudio-Ochoa Angelica, Temiakov Dmitry. . Structural basis for promoter recognition and transcription factor binding and release in human mitochondria Molecular Cell
6tz2 Aug. 9, 2019 Cui Yanxiang, Zhang Yinong, Zhou Kang, Sun Jingchen, Zhou Z. Hong. . Conservative transcription in three steps visualized in a double-stranded RNA virus Nature Structural & Molecular Biology
7n30 May 30, 2021 Rundlet Emily J., Holm Mikael, Schacherl Magdalena, Natchiar S. Kundhavai, Altman Roger B., Spahn Christian M. T., Myasnikov Alexander G., Blanchard Scott C.. . Structural basis of early translocation events on the ribosome Nature
7orj June 6, 2021 Arragain Benoît, Durieux Trouilleton Quentin, Baudin Florence, Provaznik Jan, Azevedo Nayara, Cusack Stephen, Schoehn Guy, Malet Hélène. . Structural snapshots of La Crosse virus polymerase reveal the mechanisms underlying Peribunyaviridae replication and transcription Nature Communications
8dh5 June 24, 2022 Oh Juntaek, Kimoto Michiko, Xu Haoqing, Chong Jenny, Hirao Ichiro, Wang Dong. . Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase Nature Communications
2dra June 8, 2006 Tomita Kozo, Ishitani Ryuichiro, Fukai Shuya, Nureki Osamu. . Complete crystallographic analysis of the dynamics of CCA sequence addition Nature
4q5s April 17, 2014 Basu Ritwika S., Warner Brittany A., Molodtsov Vadim, Pupov Danil, Esyunina Daria, Fernández-Tornero Carlos, Kulbachinskiy Andrey, Murakami Katsuhiko S.. . Structural Basis of Transcription Initiation by Bacterial RNA Polymerase Holoenzyme Journal of Biological Chemistry
3ovb Sept. 16, 2010 Pan Baocheng, Xiong Yong, Steitz Thomas A.. . How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA Science
1asz Jan. 19, 1995 Cavarelli J., Eriani G., Rees B., Ruff M., Boeglin M., Mitschler A., Martin F., Gangloff J., Thierry J.C., Moras D.. . The active site of yeast aspartyl‐tRNA synthetase: structural and functional aspects of the aminoacylation reaction. The EMBO Journal
7n2v May 29, 2021 Rundlet Emily J., Holm Mikael, Schacherl Magdalena, Natchiar S. Kundhavai, Altman Roger B., Spahn Christian M. T., Myasnikov Alexander G., Blanchard Scott C.. . Structural basis of early translocation events on the ribosome Nature
9ja1 Aug. 23, 2024 Ma Jianbing, Yi Gangshun, Ye Mingda, MacGregor-Chatwin Craig, Sheng Yuewen, Lu Ying, Li Ming, Li Qingrong, Wang Dong, Gilbert Robert J. C., Zhang Peijun. . Open architecture of archaea MCM and dsDNA complexes resolved using monodispersed streptavidin affinity CryoEM Nature Communications
9n2b Jan. 28, 2025 Welfer Griffin A., Brady Ryan A., Natchiar S. Kundhavai, Watson Zoe L., Rundlet Emily J., Alejo Jose L., Singh Anand P., Mishra Nitish K., Altman Roger B., Blanchard Scott C.. . Impacts of ribosomal RNA sequence variation on gene expression and phenotype Philosophical Transactions of the Royal Society B: Biological Sciences
3ovb Sept. 16, 2010 Pan Baocheng, Xiong Yong, Steitz Thomas A.. . How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA Science
8peg June 13, 2023 Flügel Timo, Schacherl Magdalena, Unbehaun Anett, Schroeer Birgit, Dabrowski Marylena, Bürger Jörg, Mielke Thorsten, Sprink Thiemo, Diebolder Christoph A., Guillén Schlippe Yollete V., Spahn Christian M. T.. . Transient disome complex formation in native polysomes during ongoing protein synthesis captured by cryo-EM Nature Communications
9sv6 Oct. 1, 2025 Li Qingrong, Yi Gangshun, Wu Yue, Xu Sophy, Chong Jenny, Huang Xuhui, Zhang Peijun, Wang Dong. . Sub-2 Å cryo-EM structures of transcribing RNA polymerase II reveal critical roles of water molecules in catalysis Molecular Cell
9n2c Jan. 28, 2025 Welfer Griffin A., Brady Ryan A., Natchiar S. Kundhavai, Watson Zoe L., Rundlet Emily J., Alejo Jose L., Singh Anand P., Mishra Nitish K., Altman Roger B., Blanchard Scott C.. . Impacts of ribosomal RNA sequence variation on gene expression and phenotype Philosophical Transactions of the Royal Society B: Biological Sciences
6uuc Oct. 30, 2019 Zuo Yuhong, De Swastik, Feng Yingang, Steitz Thomas A.. . Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation iScience
9mn6 Dec. 20, 2024 Herbine Karl, Nayak Ashok R., Zamudio-Ochoa Angelica, Temiakov Dmitry. . Structural basis for promoter recognition and transcription factor binding and release in human mitochondria Molecular Cell
8dh5 June 24, 2022 Oh Juntaek, Kimoto Michiko, Xu Haoqing, Chong Jenny, Hirao Ichiro, Wang Dong. . Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase Nature Communications
3ov7 Sept. 15, 2010 Pan Baocheng, Xiong Yong, Steitz Thomas A.. . How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA Science
8peg June 13, 2023 Flügel Timo, Schacherl Magdalena, Unbehaun Anett, Schroeer Birgit, Dabrowski Marylena, Bürger Jörg, Mielke Thorsten, Sprink Thiemo, Diebolder Christoph A., Guillén Schlippe Yollete V., Spahn Christian M. T.. . Transient disome complex formation in native polysomes during ongoing protein synthesis captured by cryo-EM Nature Communications
1gtr Sept. 15, 1993 Rould M. A., Perona J. J., Steitz T. A.. . Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase Nature
7n2u May 29, 2021 Rundlet Emily J., Holm Mikael, Schacherl Magdalena, Natchiar S. Kundhavai, Altman Roger B., Spahn Christian M. T., Myasnikov Alexander G., Blanchard Scott C.. . Structural basis of early translocation events on the ribosome Nature
7n1p May 28, 2021 Rundlet Emily J., Holm Mikael, Schacherl Magdalena, Natchiar S. Kundhavai, Altman Roger B., Spahn Christian M. T., Myasnikov Alexander G., Blanchard Scott C.. . Structural basis of early translocation events on the ribosome Nature
8dh5 June 24, 2022 Oh Juntaek, Kimoto Michiko, Xu Haoqing, Chong Jenny, Hirao Ichiro, Wang Dong. . Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase Nature Communications
7n2c May 28, 2021 Rundlet Emily J., Holm Mikael, Schacherl Magdalena, Natchiar S. Kundhavai, Altman Roger B., Spahn Christian M. T., Myasnikov Alexander G., Blanchard Scott C.. . Structural basis of early translocation events on the ribosome Nature
8u9x Sept. 20, 2023 Lin Guowu, Barnes Christopher O., Weiss Simon, Dutagaci Bercem, Qiu Chenxi, Feig Michael, Song Jihnu, Lyubimov Artem, Cohen Aina E., Kaplan Craig D., Calero Guillermo. . Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser Proceedings of the National Academy of Sciences
6zxg July 29, 2020 Ameismeier Michael, Zemp Ivo, van den Heuvel Jasmin, Thoms Matthias, Berninghausen Otto, Kutay Ulrike, Beckmann Roland. . Structural basis for the final steps of human 40S ribosome maturation Nature
7n2c May 28, 2021 Rundlet Emily J., Holm Mikael, Schacherl Magdalena, Natchiar S. Kundhavai, Altman Roger B., Spahn Christian M. T., Myasnikov Alexander G., Blanchard Scott C.. . Structural basis of early translocation events on the ribosome Nature
8u9r Sept. 20, 2023 Lin Guowu, Barnes Christopher O., Weiss Simon, Dutagaci Bercem, Qiu Chenxi, Feig Michael, Song Jihnu, Lyubimov Artem, Cohen Aina E., Kaplan Craig D., Calero Guillermo. . Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser Proceedings of the National Academy of Sciences
1n77 Nov. 13, 2002 Sekine Shun‐ichi, Nureki Osamu, Dubois Daniel Y., Bernier Stéphane, Chênevert Robert, Lapointe Jacques, Vassylyev Dmitry G., Yokoyama Shigeyuki. . ATP binding by glutamyl‐tRNA synthetase is switched to the productive mode by tRNA binding The EMBO Journal
2zh6 Feb. 1, 2008 Toh Yukimatsu, Numata Tomoyuki, Watanabe Kazunori, Takeshita Daijiro, Nureki Osamu, Tomita Kozo. . Molecular basis for maintenance of fidelity during the CCA‐adding reaction by a CCA‐adding enzyme The EMBO Journal

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 507.18 g/mol
HBA not available
HBD not available
HBA + HBD
AlogP not available
TPSA not available
RB not available

Radar chart