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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
1p52 ADP Arginine kinase 2.7.3.3

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1p52 ADPArginine kinase 2.7.3.3 1.185
4gvz ADPArginine kinase 2.7.3.3 1.025
3jq3 ADPLombricine kinase / 0.860
4o6n CDPUncharacterized protein / 0.690
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.681
2rgx AP5Adenylate kinase / 0.678
4dwb 0M7Farnesyl pyrophosphate synthase / 0.678
1oe0 TTPDeoxynucleoside kinase / 0.674
3mhy ATPNitrogen regulatory protein P-II 1 / 0.668
1p3j AP5Adenylate kinase / 0.666
3pff ADPATP-citrate synthase 2.3.3.8 0.666
4rf9 AGSArginine kinase 2.7.3.3 0.665
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.663
4to3 DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.662
3e39 FMNNitroreductase / 0.661
4qfy DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.660
1q3s ADPThermosome subunit alpha / 0.659
3orl AGSSerine/threonine protein kinase / 0.659
4to4 DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.659
4dxj 0M9Farnesyl pyrophosphate synthase / 0.657
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.655
3vqv ANPPyrrolysine--tRNA ligase / 0.655
2vp0 TTPDeoxynucleoside kinase / 0.653
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.652
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.651
3rbm B73Farnesyl pyrophosphate synthase, putative / 0.651
2xul ATPNitrogen regulatory protein P-II / 0.650
3vth APCCarbamoyltransferase / 0.650