HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound PRF

Identifiers

  • Canonical SMILES: 
    NCc1c[nH]c2N=C(N)NC(=O)c12
  • IUPAC name: 
    2-amino-5-(aminomethyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
  • InChi: 
    InChI=1S/C7H9N5O/c8-1-3-2-10-5-4(3)6(13)12-7(9)11-5/h2H,1,8H2,(H4,9,10,11,12,13)
  • InChiKey: 
    MEYMBLGOKYDGLZ-UHFFFAOYSA-N

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

171 CHEMBL1235432 DB03304

RNA-SM complexes

PDB code Deposition date Reference publication
2l1v Aug. 6, 2010 Kang Mijeong, Peterson Robert, Feigon Juli. . Structural Insights into Riboswitch Control of the Biosynthesis of Queuosine, a Modified Nucleotide Found in the Anticodon of tRNA Molecular Cell
2miy Dec. 20, 2013 Kang Mijeong, Eichhorn Catherine D., Feigon Juli. . Structural determinants for ligand capture by a class II preQ 1 riboswitch Proceedings of the National Academy of Sciences
3fu2 Jan. 13, 2009 Klein Daniel J, Edwards Thomas E, Ferré-D'Amaré Adrian R. . Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase Nature Structural & Molecular Biology
3fu2 Jan. 13, 2009 Klein Daniel J, Edwards Thomas E, Ferré-D'Amaré Adrian R. . Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase Nature Structural & Molecular Biology
3fu2 Jan. 13, 2009 Klein Daniel J, Edwards Thomas E, Ferré-D'Amaré Adrian R. . Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase Nature Structural & Molecular Biology
3k1v Sept. 28, 2009 Klein Daniel J, Edwards Thomas E, Ferré-D'Amaré Adrian R. . Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase Nature Structural & Molecular Biology
3q50 Dec. 26, 2010 Jenkins Jermaine L., Krucinska Jolanta, McCarty Reid M., Bandarian Vahe, Wedekind Joseph E.. . Comparison of a PreQ1 Riboswitch Aptamer in Metabolite-bound and Free States with Implications for Gene Regulation Journal of Biological Chemistry
4jf2 Feb. 27, 2013 Liberman Joseph A, Salim Mohammad, Krucinska Jolanta, Wedekind Joseph E. . Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold Nature Chemical Biology
4rzd Dec. 20, 2014 Liberman Joseph A., Suddala Krishna C., Aytenfisu Asaminew, Chan Dalen, Belashov Ivan A., Salim Mohammad, Mathews David H., Spitale Robert C., Walter Nils G., Wedekind Joseph E.. . Structural analysis of a class III preQ 1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics Proceedings of the National Academy of Sciences
5d5l Aug. 10, 2015
5d5l Aug. 10, 2015
5d5l Aug. 10, 2015
5d5l Aug. 10, 2015
6vui Feb. 15, 2020 Schroeder Griffin M, Dutta Debapratim, Cavender Chapin E, Jenkins Jermaine L, Pritchett Elizabeth M, Baker Cameron D, Ashton John M, Mathews David H, Wedekind Joseph E. . Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation Nucleic Acids Research
6xkn June 26, 2020 Srivastava Yoshita, Akinyemi Olayinka, Rohe Tiana C, Pritchett Elizabeth M, Baker Cameron D, Sharma Akshara, Jenkins Jermaine L, Mathews David H, Wedekind Joseph E. . Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations Nucleic Acids Research
6xko June 26, 2020 Srivastava Yoshita, Akinyemi Olayinka, Rohe Tiana C, Pritchett Elizabeth M, Baker Cameron D, Sharma Akshara, Jenkins Jermaine L, Mathews David H, Wedekind Joseph E. . Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations Nucleic Acids Research
8fza Jan. 27, 2023 Schroeder Griffin M., Kiliushik Daniil, Jenkins Jermaine L., Wedekind Joseph E.. . Structure and function analysis of a type III preQ1-I riboswitch from Escherichia coli reveals direct metabolite sensing by the Shine-Dalgarno sequence Journal of Biological Chemistry
8fza Jan. 27, 2023 Schroeder Griffin M., Kiliushik Daniil, Jenkins Jermaine L., Wedekind Joseph E.. . Structure and function analysis of a type III preQ1-I riboswitch from Escherichia coli reveals direct metabolite sensing by the Shine-Dalgarno sequence Journal of Biological Chemistry
8g4w Feb. 10, 2023 Chauvier Adrien, Porta Jason C., Deb Indrajit, Ellinger Emily, Meze Katarina, Frank Aaron T., Ohi Melanie D., Walter Nils G.. . Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand Nature Structural & Molecular Biology
8g7e Feb. 16, 2023 Chauvier Adrien, Porta Jason C., Deb Indrajit, Ellinger Emily, Meze Katarina, Frank Aaron T., Ohi Melanie D., Walter Nils G.. . Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand Nature Structural & Molecular Biology
8g8z Feb. 20, 2023 Chauvier Adrien, Porta Jason C., Deb Indrajit, Ellinger Emily, Meze Katarina, Frank Aaron T., Ohi Melanie D., Walter Nils G.. . Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand Nature Structural & Molecular Biology
8toz Aug. 4, 2023 Srivastava Yoshita, Akinyemi Olayinka, Rohe Tiana C, Pritchett Elizabeth M, Baker Cameron D, Sharma Akshara, Jenkins Jermaine L, Mathews David H, Wedekind Joseph E. . Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations Nucleic Acids Research
8vpv Jan. 17, 2024 Srivastava Yoshita, Akinyemi Olayinka, Rohe Tiana C, Pritchett Elizabeth M, Baker Cameron D, Sharma Akshara, Jenkins Jermaine L, Mathews David H, Wedekind Joseph E. . Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations Nucleic Acids Research

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 179.08 g/mol
HBA 4
HBD 4
HBA + HBD
AlogP -0.71
TPSA 113.58
RB 1

Radar chart