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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
4okk U5P 3'-5' exoribonuclease MT2234.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4okk U5P3'-5' exoribonuclease MT2234.1 / 0.921
1g7u PEP2-dehydro-3-deoxyphosphooctonate aldolase 2.5.1.55 0.744
3b6p TMPThree-prime repair exonuclease 1 3.1.11.2 0.726
2o4g TMPThree-prime repair exonuclease 1 3.1.11.2 0.724
3s6a ANPAdenosine monophosphate-protein transferase NmFic 2.7.7.n1 0.670
1v25 ANPLong-chain-fatty-acid--CoA ligase 6.2.1.3 0.666
3tw6 ADPPyruvate carboxylase / 0.665
2p0a ANPSynapsin-3 / 0.661
2az3 CDPNucleoside diphosphate kinase / 0.659
4pb1 RBVNucleoside permease / 0.656
4pda CTNNucleoside permease / 0.656
4gnc ASORegucalcin 3.1.1.17 0.654
3zcn ATPAdenosine monophosphate-protein transferase SoFic 2.7.7.n1 0.653
2ikf UTPPoly(A) polymerase, putative / 0.652
1s16 ANPDNA topoisomerase 4 subunit B / 0.651
4fh5 UTPTerminal uridylyltransferase cid1 / 0.651
4ube 2FAAdenosine kinase 2.7.1.20 0.651
2ido TMPDNA polymerase III subunit epsilon 2.7.7.7 0.650