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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
3q8uADPNucleoside diphosphate kinase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3q8uADPNucleoside diphosphate kinase/1.000
2dxdANPNucleoside diphosphate kinase2.7.4.60.523
1nhkCMPNucleoside diphosphate kinase2.7.4.60.508
4hr2ADPNucleoside diphosphate kinase/0.499
1zs6ADPNucleoside diphosphate kinase 32.7.4.60.486
2hveADPNucleoside diphosphate kinase A2.7.4.60.480
1nueGDPNucleoside diphosphate kinase B2.7.4.60.474
1buxPPSNucleoside diphosphate kinase, cytosolic2.7.4.60.463
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.454
1wklATPNucleoside diphosphate kinase/0.452
4uohADPNucleoside diphosphate kinase/0.448
3nguADPNucleoside diphosphate kinase/0.444