HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound C2E

Identifiers

  • Canonical SMILES: 
    NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@H]5[C@@H](O)[C@@H](O[C@@H]5CO[P](O)(=O)O[C@H]4[C@H]3O)n6cnc7C(=O)NC(=Nc67)N
  • IUPAC name: 
    9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
  • InChi: 
    InChI=1S/C20H24N10O14P2/c21-19-25-13-7(15(33)27-19)23-3-29(13)17-9(31)11-5(41-17)1-39-45(35,36)44-12-6(2-40-46(37,38)43-11)42-18(10(12)32)30-4-24-8-14(30)26-20(22)28-16(8)34/h3-6,9-12,17-18,31-32H,1-2H2,(H,35,36)(H,37,38)(H3,21,25,27,33)(H3,22,26,28,34)/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1
  • InChiKey: 
    PKFDLKSEZWEFGL-MHARETSRSA-N

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

135440063 CHEMBL1231573

RNA-SM complexes

PDB code Deposition date Reference publication
3irw Aug. 24, 2009 Smith Kathryn D, Lipchock Sarah V, Ames Tyler D, Wang Jimin, Breaker Ronald R, Strobel Scott A. . Structural basis of ligand binding by a c-di-GMP riboswitch Nature Structural & Molecular Biology
3iwn Sept. 2, 2009 Kulshina Nadia, Baird Nathan J, Ferré-D'Amaré Adrian R. . Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch Nature Structural & Molecular Biology
3iwn Sept. 2, 2009 Kulshina Nadia, Baird Nathan J, Ferré-D'Amaré Adrian R. . Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch Nature Structural & Molecular Biology
3mum May 3, 2010 Smith Kathryn D., Lipchock Sarah V., Livingston Alison L., Shanahan Carly A., Strobel Scott A.. . Structural and Biochemical Determinants of Ligand Binding by the c-di-GMP Riboswitch, Biochemistry
3mur May 3, 2010 Smith Kathryn D., Lipchock Sarah V., Livingston Alison L., Shanahan Carly A., Strobel Scott A.. . Structural and Biochemical Determinants of Ligand Binding by the c-di-GMP Riboswitch, Biochemistry
3mut May 3, 2010 Smith Kathryn D., Lipchock Sarah V., Livingston Alison L., Shanahan Carly A., Strobel Scott A.. . Structural and Biochemical Determinants of Ligand Binding by the c-di-GMP Riboswitch, Biochemistry
3mxh May 7, 2010 Smith Kathryn D., Lipchock Sarah V., Livingston Alison L., Shanahan Carly A., Strobel Scott A.. . Structural and Biochemical Determinants of Ligand Binding by the c-di-GMP Riboswitch, Biochemistry
3q3z Dec. 22, 2010 Smith Kathryn D., Shanahan Carly A., Moore Emily L., Simon Aline C., Strobel Scott A.. . Structural basis of differential ligand recognition by two classes of bis-(3′-5′)-cyclic dimeric guanosine monophosphate-binding riboswitches Proceedings of the National Academy of Sciences
3q3z Dec. 22, 2010 Smith Kathryn D., Shanahan Carly A., Moore Emily L., Simon Aline C., Strobel Scott A.. . Structural basis of differential ligand recognition by two classes of bis-(3′-5′)-cyclic dimeric guanosine monophosphate-binding riboswitches Proceedings of the National Academy of Sciences
3q3z Dec. 22, 2010 Smith Kathryn D., Shanahan Carly A., Moore Emily L., Simon Aline C., Strobel Scott A.. . Structural basis of differential ligand recognition by two classes of bis-(3′-5′)-cyclic dimeric guanosine monophosphate-binding riboswitches Proceedings of the National Academy of Sciences
3q3z Dec. 22, 2010 Smith Kathryn D., Shanahan Carly A., Moore Emily L., Simon Aline C., Strobel Scott A.. . Structural basis of differential ligand recognition by two classes of bis-(3′-5′)-cyclic dimeric guanosine monophosphate-binding riboswitches Proceedings of the National Academy of Sciences
4yb0 Feb. 18, 2015 Ren Aiming, Wang Xin C., Kellenberger Colleen A., Rajashankar Kanagalaghatta R., Jones Roger A., Hammond Ming C., Patel Dinshaw J.. . Structural Basis for Molecular Discrimination by a 3′,3′-cGAMP Sensing Riboswitch Cell Reports
4yb0 Feb. 18, 2015 Ren Aiming, Wang Xin C., Kellenberger Colleen A., Rajashankar Kanagalaghatta R., Jones Roger A., Hammond Ming C., Patel Dinshaw J.. . Structural Basis for Molecular Discrimination by a 3′,3′-cGAMP Sensing Riboswitch Cell Reports

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 690.10 g/mol
HBA 20
HBD 8
HBA + HBD
AlogP -3.05
TPSA 349.62
RB 2

Radar chart