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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
2dxe GDP Nucleoside diphosphate kinase 2.7.4.6

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2dxe GDPNucleoside diphosphate kinase 2.7.4.6 1.168
2dy9 ADPNucleoside diphosphate kinase 2.7.4.6 1.102
4fkx CDPNucleoside diphosphate kinase / 0.897
4uof DATNucleoside diphosphate kinase / 0.843
4uoh ADPNucleoside diphosphate kinase / 0.838
3bbf GDPNucleoside diphosphate kinase B 2.7.4.6 0.816
2dxf GNPNucleoside diphosphate kinase 2.7.4.6 0.808
2hve ADPNucleoside diphosphate kinase A 2.7.4.6 0.806
1nue GDPNucleoside diphosphate kinase B 2.7.4.6 0.789
1zs6 ADPNucleoside diphosphate kinase 3 2.7.4.6 0.785
4uog YYYNucleoside diphosphate kinase / 0.757
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.749
2hvd ADPNucleoside diphosphate kinase A 2.7.4.6 0.746
2az3 CDPNucleoside diphosphate kinase / 0.738
3ngu ADPNucleoside diphosphate kinase / 0.703
4hr2 ADPNucleoside diphosphate kinase / 0.685
1vp6 CMPCyclic nucleotide-gated potassium channel mll3241 / 0.683
1be4 PCGNucleoside diphosphate kinase A 2 2.7.4.6 0.681
1lwx AZDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.681
4o6n CDPUncharacterized protein / 0.662
2ydo ADNAdenosine receptor A2a / 0.659
4ku7 PCGcGMP-dependent protein kinase 1 2.7.11.12 0.659
4i0b CMPcAMP-activated global transcriptional regulator CRP / 0.657
4s1b 2BALmo1466 protein / 0.657
4kh0 ATPAspartate carbamoyltransferase regulatory chain {ECO:0000256|HAMAP-Rule:MF_00002} / 0.656
4yb7 ATPATP phosphoribosyltransferase / 0.654
1cgp CMPcAMP-activated global transcriptional regulator CRP / 0.653
2ikf UTPPoly(A) polymerase, putative / 0.652