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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
2ncd ADP Protein claret segregational

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2ncd ADPProtein claret segregational / 0.896
4b7b ADPKinesin-like protein KIF11 / 0.725
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.721
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.704
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.701
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.691
3thy ADPDNA mismatch repair protein Msh2 / 0.691
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.687
2zro ADPProtein RecA / 0.681
4dsu GDPGTPase KRas / 0.681
1w5s ADPORC1-type DNA replication protein 2 / 0.676
2x2r ADPKinesin-like protein KIF11 / 0.676
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.673
2whx ADPGenome polyprotein 3.4.21.91 0.670
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.667
2gm1 ADPKinesin-like protein KIF11 / 0.666
3ref GDPRho family GTPase / 0.666
1z0a GDPRas-related protein Rab-2A / 0.665
4epw GDPGTPase KRas / 0.664
1z0f GDPRas-related protein Rab-14 / 0.663
4lv6 GDPGTPase KRas / 0.661
4o2r GDPGTP-binding protein Rheb / 0.661
4wa7 GDPGTPase KRas / 0.661
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.660
3x1w GDPRas-related protein Rap-1b / 0.660
4q02 GDPGTPase KRas / 0.660
4q03 GDPGTPase KRas / 0.660
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.659
1sq5 ADPPantothenate kinase 2.7.1.33 0.659
4ldj GDPGTPase KRas / 0.659
4epx GDPGTPase KRas / 0.658
1yra GDPGPN-loop GTPase PAB0955 / 0.656
2dpx GDPGTP-binding protein RAD / 0.656
3q5d GDPAtlastin-1 3.6.5 0.656
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.652
1svl ADPLarge T antigen 3.6.4 0.652
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.651
4iei ADPGene 2 protein / 0.650