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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
3zu0 A12 NAD 5'-nucleotidase 3.1.3.5

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3zu0 A12NAD 5'-nucleotidase 3.1.3.5 1.124
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.677
3tw6 ADPPyruvate carboxylase / 0.673
2npn SAMPutative cobalamin synthesis related protein / 0.671
3cr3 ADPPTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL 2.7 0.669
1ho5 ADNProtein UshA 3.1.3.5 0.665
2q7h YLYPyrrolysine--tRNA ligase / 0.663
2eka SAHDiphthine synthase / 0.658
2zbv ADNUncharacterized protein / 0.658
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.658
4ts7 ADPPurine phosphoribosyltransferase (GpT-1) / 0.656
4q7f 3D1Uncharacterized protein / 0.655
2v92 ATP5'-AMP-activated protein kinase subunit gamma-1 / 0.654
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 0.654
4uhr NGIAdenosine receptor A2a / 0.653
2dv3 SAHDiphthine synthase / 0.652
2ed5 SAHDiphthine synthase / 0.652
2pch SAHDiphthine synthase / 0.652
1olt SAMOxygen-independent coproporphyrinogen III oxidase / 0.651
2el3 SAHDiphthine synthase / 0.651
2p5c SAHDiphthine synthase / 0.651
2pb5 SAHDiphthine synthase / 0.650