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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
2dxf GNP Nucleoside diphosphate kinase 2.7.4.6

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2dxf GNPNucleoside diphosphate kinase 2.7.4.6 0.851
2dxe GDPNucleoside diphosphate kinase 2.7.4.6 0.808
1g7u PEP2-dehydro-3-deoxyphosphooctonate aldolase 2.5.1.55 0.744
4e5i 0N9Polymerase acidic protein / 0.744
1nue GDPNucleoside diphosphate kinase B 2.7.4.6 0.720
1zs6 ADPNucleoside diphosphate kinase 3 2.7.4.6 0.715
2dy9 ADPNucleoside diphosphate kinase 2.7.4.6 0.715
3bbf GDPNucleoside diphosphate kinase B 2.7.4.6 0.704
4uof DATNucleoside diphosphate kinase / 0.699
1be4 PCGNucleoside diphosphate kinase A 2 2.7.4.6 0.691
4uoh ADPNucleoside diphosphate kinase / 0.683
2hvd ADPNucleoside diphosphate kinase A 2.7.4.6 0.678
4hr2 ADPNucleoside diphosphate kinase / 0.676
4uog YYYNucleoside diphosphate kinase / 0.671
4hbn CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 / 0.666
4fkx CDPNucleoside diphosphate kinase / 0.665
4e5f 0N7Polymerase acidic protein / 0.660
1vp6 CMPCyclic nucleotide-gated potassium channel mll3241 / 0.653
2az3 CDPNucleoside diphosphate kinase / 0.653
3otf CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 / 0.651
4i02 CMPcAMP-activated global transcriptional regulator CRP / 0.651
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.650
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650
3rl3 5GPMetallophosphoesterase MPPED2 3.1 0.650
3rou CMPcAMP-activated global transcriptional regulator CRP / 0.650