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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
3mvw BHZ Nickel-binding periplasmic protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3mvw BHZNickel-binding periplasmic protein / 1.067
3mw0 BHRNickel-binding periplasmic protein / 0.956
3mzb BHRNickel-binding periplasmic protein / 0.910
3mz9 BHNNickel-binding periplasmic protein / 0.743
3mvz BHNNickel-binding periplasmic protein / 0.718
3mvy BHZNickel-binding periplasmic protein / 0.716
3ar4 ATPSarcoplasmic/endoplasmic reticulum calcium ATPase 1 3.6.3.8 0.686
3s8a DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.686
3tb9 ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.684
3s87 DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.682
2cvx DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.681
3k8t DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.680
2o1o RISPutative farnesyl pyrophosphate synthase / 0.677
2cvu ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.676
3zcb ATPAdenosine monophosphate-protein transferase VbhT 2.7.7.n1 0.668
1x09 IPEDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) 2.5.1.31 0.666
2aky AP5Adenylate kinase / 0.658
2r2n KYNKynurenine/alpha-aminoadipate aminotransferase, mitochondrial 2.6.1.39 0.658
1n38 U3HRNA-directed RNA polymerase lambda-3 2.7.7.48 0.656
3o5t ADPNitrogen regulatory protein P-II 1 / 0.654
3uwq U5POrotidine 5'-phosphate decarboxylase / 0.654
5cc9 DDFDihydrofolate reductase 1.5.1.3 0.653
1e26 GPBDihydrofolate reductase 1.5.1.3 0.652
4fag GTQGentisate 1,2-dioxygenase / 0.652
4bri UNPEctonucleoside triphosphate diphosphohydrolase I / 0.651
3ewy U5PUridine 5'-monophosphate synthase 4.1.1.23 0.650