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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
4fkx CDP Nucleoside diphosphate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4fkx CDPNucleoside diphosphate kinase / 1.062
4uoh ADPNucleoside diphosphate kinase / 0.936
4uof DATNucleoside diphosphate kinase / 0.919
2dxe GDPNucleoside diphosphate kinase 2.7.4.6 0.897
4uog YYYNucleoside diphosphate kinase / 0.867
1nue GDPNucleoside diphosphate kinase B 2.7.4.6 0.859
2dy9 ADPNucleoside diphosphate kinase 2.7.4.6 0.837
3bbf GDPNucleoside diphosphate kinase B 2.7.4.6 0.802
2az3 CDPNucleoside diphosphate kinase / 0.798
3ngu ADPNucleoside diphosphate kinase / 0.793
2hve ADPNucleoside diphosphate kinase A 2.7.4.6 0.789
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.772
1zs6 ADPNucleoside diphosphate kinase 3 2.7.4.6 0.771
2hvd ADPNucleoside diphosphate kinase A 2.7.4.6 0.759
4hr2 ADPNucleoside diphosphate kinase / 0.716
2cvx DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.704
3s87 DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.702
3q8u ADPNucleoside diphosphate kinase / 0.700
1lwx AZDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.694
4qm6 GTPMetallophosphoesterase / 0.691
1peq TTPRibonucleoside-diphosphate reductase 2 subunit alpha 1.17.4.1 0.689
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.685
1nhk CMPNucleoside diphosphate kinase 2.7.4.6 0.683
1vp6 CMPCyclic nucleotide-gated potassium channel mll3241 / 0.672
2dxf GNPNucleoside diphosphate kinase 2.7.4.6 0.665
4dld TZGGlutamate receptor ionotropic, kainate 1 / 0.664
2p0a ANPSynapsin-3 / 0.662
4hbn CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 / 0.662
1jje BYSBeta-lactamase / 0.660
2w5a ADPSerine/threonine-protein kinase Nek2 2.7.11.1 0.659
4u0z APCAdenosine monophosphate-protein transferase FICD 2.7.7.n1 0.658
4fvq ATPTyrosine-protein kinase JAK2 / 0.655
4i0b CMPcAMP-activated global transcriptional regulator CRP / 0.654
4r8h SP1cAMP-activated global transcriptional regulator CRP / 0.654
4yb7 ATPATP phosphoribosyltransferase / 0.654
1xje GDPVitamin B12-dependent ribonucleotide reductase / 0.653
1rgs CMPcAMP-dependent protein kinase type I-alpha regulatory subunit / 0.651
4ube 2FAAdenosine kinase 2.7.1.20 0.650