HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound APC

Identifiers

  • Canonical SMILES: 
    Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  • IUPAC name: 
    5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine
  • InChi: 
    InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1
  • InChiKey: 
    CAWZRIXWFRFUQB-IOSLPCCCSA-N
  • SMARTS: 
    [#7]-[#6]1:[#7]:[#6]:[#7]:[#6]2:[#7](:[#6]:[#7]:[#6]:1:2)-[#6@@H]1-[#8]-[#6@H](-[#6]-[#8]-[#15@@](-[#8])(=[#8])-[#6]-[#15@@](-[#8])(=[#8])-[#8]-[#15](-[#8])(-[#8])=[#8])-[#6@@H](-[#8])-[#6@H]-1-[#8]

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

91557 CHEMBL132722 DB02596

RNA-SM complexes

PDB code Deposition date Reference publication
1s0v Jan. 5, 2004 Temiakov Dmitry, Patlan Vsevolod, Anikin Michael, McAllister William T, Yokoyama Shigeyuki, Vassylyev Dmitry G. . Structural Basis for Substrate Selection by T7 RNA Polymerase Cell
1s0v Jan. 5, 2004 Temiakov Dmitry, Patlan Vsevolod, Anikin Michael, McAllister William T, Yokoyama Shigeyuki, Vassylyev Dmitry G. . Structural Basis for Substrate Selection by T7 RNA Polymerase Cell
1s0v Jan. 5, 2004 Temiakov Dmitry, Patlan Vsevolod, Anikin Michael, McAllister William T, Yokoyama Shigeyuki, Vassylyev Dmitry G. . Structural Basis for Substrate Selection by T7 RNA Polymerase Cell
1s0v Jan. 5, 2004 Temiakov Dmitry, Patlan Vsevolod, Anikin Michael, McAllister William T, Yokoyama Shigeyuki, Vassylyev Dmitry G. . Structural Basis for Substrate Selection by T7 RNA Polymerase Cell
1s76 Jan. 29, 2004 Yin Y.Whitney, Steitz Thomas A. . The Structural Mechanism of Translocation and Helicase Activity in T7 RNA Polymerase Cell
1vfg April 13, 2004 Tomita Kozo, Fukai Shuya, Ishitani Ryuichiro, Ueda Takuya, Takeuchi Nono, Vassylyev Dmitry G., Nureki Osamu. . Structural basis for template-independent RNA polymerization Nature
2o5j Dec. 6, 2006 Vassylyev Dmitry G., Vassylyeva Marina N., Zhang Jinwei, Palangat Murali, Artsimovitch Irina, Landick Robert. . Structural basis for substrate loading in bacterial RNA polymerase Nature
2o5j Dec. 6, 2006 Vassylyev Dmitry G., Vassylyeva Marina N., Zhang Jinwei, Palangat Murali, Artsimovitch Irina, Landick Robert. . Structural basis for substrate loading in bacterial RNA polymerase Nature
2ppb April 28, 2007 Vassylyev Dmitry G., Vassylyeva Marina N., Zhang Jinwei, Palangat Murali, Artsimovitch Irina, Landick Robert. . Structural basis for substrate loading in bacterial RNA polymerase Nature
2ppb April 28, 2007 Vassylyev Dmitry G., Vassylyeva Marina N., Zhang Jinwei, Palangat Murali, Artsimovitch Irina, Landick Robert. . Structural basis for substrate loading in bacterial RNA polymerase Nature
3amu Aug. 23, 2010 Osawa Takuo, Kimura Satoshi, Terasaka Naohiro, Inanaga Hideko, Suzuki Tsutomu, Numata Tomoyuki. . Structural basis of tRNA agmatinylation essential for AUA codon decoding Nature Structural & Molecular Biology
3ova 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
4a3e Sept. 30, 2011 Cheung Alan C M, Sainsbury Sarah, Cramer Patrick. . Structural basis of initial RNA polymerase II transcription The EMBO Journal
4a3f Sept. 30, 2011 Cheung Alan C M, Sainsbury Sarah, Cramer Patrick. . Structural basis of initial RNA polymerase II transcription The EMBO Journal
4a3l Sept. 30, 2011 Cheung Alan C M, Sainsbury Sarah, Cramer Patrick. . Structural basis of initial RNA polymerase II transcription The EMBO Journal
4a3m Sept. 30, 2011 Cheung Alan C M, Sainsbury Sarah, Cramer Patrick. . Structural basis of initial RNA polymerase II transcription The EMBO Journal
4by1 July 17, 2013 Kinkelin Kerstin, Wozniak Glenn G., Rothbart Scott B., Lidschreiber Michael, Strahl Brian D., Cramer Patrick. . Structures of RNA polymerase II complexes with Bye1, a chromatin-binding PHF3/DIDO homologue Proceedings of the National Academy of Sciences
4wc2 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
4x4r Dec. 3, 2014 Kuhn Claus-D., Wilusz Jeremy E., Zheng Yuxuan, Beal Peter A., Joshua-Tor Leemor. . On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme Cell
4x4r Dec. 3, 2014 Kuhn Claus-D., Wilusz Jeremy E., Zheng Yuxuan, Beal Peter A., Joshua-Tor Leemor. . On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme Cell
4x4u Dec. 3, 2014 Kuhn Claus-D., Wilusz Jeremy E., Zheng Yuxuan, Beal Peter A., Joshua-Tor Leemor. . On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme Cell
4x4u Dec. 3, 2014 Kuhn Claus-D., Wilusz Jeremy E., Zheng Yuxuan, Beal Peter A., Joshua-Tor Leemor. . On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme Cell
4x4v Dec. 3, 2014 Kuhn Claus-D., Wilusz Jeremy E., Zheng Yuxuan, Beal Peter A., Joshua-Tor Leemor. . On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme Cell
4x4v Dec. 3, 2014 Kuhn Claus-D., Wilusz Jeremy E., Zheng Yuxuan, Beal Peter A., Joshua-Tor Leemor. . On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme Cell
5xog May 28, 2017 Ehara Haruhiko, Yokoyama Takeshi, Shigematsu Hideki, Yokoyama Shigeyuki, Shirouzu Mikako, Sekine Shun-ichi. . Structure of the complete elongation complex of RNA polymerase II with basal factors Science
6blp Nov. 11, 2017 Wang Wei, Walmacq Celine, Chong Jenny, Kashlev Mikhail, Wang Dong. . Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II Proceedings of the National Academy of Sciences
6upy Oct. 18, 2019 Oh Juntaek, Fleming Aaron M., Xu Jun, Chong Jenny, Burrows Cynthia J., Wang Dong. . RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair–π and CH–π interactions Proceedings of the National Academy of Sciences
8u8u Sept. 18, 2023 Herbine Karl, Nayak Ashok R., Temiakov Dmitry. . Structural basis for substrate binding and selection by human mitochondrial RNA polymerase Nature Communications
8u8v Sept. 18, 2023 Herbine Karl, Nayak Ashok R., Temiakov Dmitry. . Structural basis for substrate binding and selection by human mitochondrial RNA polymerase Nature Communications
9bdd April 11, 2024 Herbine Karl, Nayak Ashok R., Temiakov Dmitry. . Structural basis for substrate binding and selection by human mitochondrial RNA polymerase Nature Communications
9g23 July 10, 2024 Santos-Aledo Alicia, Plaza-Pegueroles Adrián, Sanz-Murillo Marta, Ruiz Federico M., Hou Peini, Xu Jun, Gil-Carton David, Wang Dong, Fernández-Tornero Carlos. . Cryo-EM uncovers a sequential mechanism for RNA polymerase I pausing and stalling at abasic DNA lesions Nature Communications
9n5e 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

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 505.02 g/mol
HBA 12
HBD 7
HBA + HBD
AlogP -1.52
TPSA 269.90
RB 8

Radar chart