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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
2dy9 ADP Nucleoside diphosphate kinase 2.7.4.6

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2dy9 ADPNucleoside diphosphate kinase 2.7.4.6 1.168
2dxe GDPNucleoside diphosphate kinase 2.7.4.6 1.102
4fkx CDPNucleoside diphosphate kinase / 0.837
4uoh ADPNucleoside diphosphate kinase / 0.835
4uof DATNucleoside diphosphate kinase / 0.828
3bbf GDPNucleoside diphosphate kinase B 2.7.4.6 0.826
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.808
1zs6 ADPNucleoside diphosphate kinase 3 2.7.4.6 0.800
1nue GDPNucleoside diphosphate kinase B 2.7.4.6 0.777
2hve ADPNucleoside diphosphate kinase A 2.7.4.6 0.755
4uog YYYNucleoside diphosphate kinase / 0.750
2hvd ADPNucleoside diphosphate kinase A 2.7.4.6 0.742
2az3 CDPNucleoside diphosphate kinase / 0.731
2dxf GNPNucleoside diphosphate kinase 2.7.4.6 0.715
3q8u ADPNucleoside diphosphate kinase / 0.702
1lwx AZDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.695
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.670
1rgs CMPcAMP-dependent protein kinase type I-alpha regulatory subunit / 0.666
3ngu ADPNucleoside diphosphate kinase / 0.666
4s1b 2BALmo1466 protein / 0.665
1hw5 CMPcAMP-activated global transcriptional regulator CRP / 0.657
1cgp CMPcAMP-activated global transcriptional regulator CRP / 0.656
1g6n CMPcAMP-activated global transcriptional regulator CRP / 0.654
2pja 33ZCarboxypeptidase B / 0.653
2ptm CMPHyperpolarization-activated (Ih) channel / 0.651
4x2d ATPFic family protein putative filamentation induced by cAMP protein / 0.651
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.650