Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
3bbf GDP Nucleoside diphosphate kinase B 2.7.4.6

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3bbf GDPNucleoside diphosphate kinase B 2.7.4.6 1.049
1nue GDPNucleoside diphosphate kinase B 2.7.4.6 0.877
4uoh ADPNucleoside diphosphate kinase / 0.872
4uof DATNucleoside diphosphate kinase / 0.871
2dy9 ADPNucleoside diphosphate kinase 2.7.4.6 0.826
4uog YYYNucleoside diphosphate kinase / 0.822
2dxe GDPNucleoside diphosphate kinase 2.7.4.6 0.816
2hvd ADPNucleoside diphosphate kinase A 2.7.4.6 0.803
4fkx CDPNucleoside diphosphate kinase / 0.802
1zs6 ADPNucleoside diphosphate kinase 3 2.7.4.6 0.800
2hve ADPNucleoside diphosphate kinase A 2.7.4.6 0.793
2dxf GNPNucleoside diphosphate kinase 2.7.4.6 0.704
3q8u ADPNucleoside diphosphate kinase / 0.694
4hr2 ADPNucleoside diphosphate kinase / 0.691
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.682
1vp6 CMPCyclic nucleotide-gated potassium channel mll3241 / 0.673
2az3 CDPNucleoside diphosphate kinase / 0.671
1be4 PCGNucleoside diphosphate kinase A 2 2.7.4.6 0.668
3rl3 5GPMetallophosphoesterase MPPED2 3.1 0.653
4mgi CMPRap guanine nucleotide exchange factor 4 / 0.653