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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
3mw0 BHR Nickel-binding periplasmic protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3mw0 BHRNickel-binding periplasmic protein / 1.113
3mzb BHRNickel-binding periplasmic protein / 1.023
3mvw BHZNickel-binding periplasmic protein / 0.956
3mvz BHNNickel-binding periplasmic protein / 0.867
3mvy BHZNickel-binding periplasmic protein / 0.834
3mz9 BHNNickel-binding periplasmic protein / 0.735
3q6j KPC2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.687
3tb9 ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.683
3s87 DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.682
2cvx DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.679
3k8t DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.678
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.673
2cvu ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.672
2e82 IM3D-amino-acid oxidase 1.4.3.3 0.672
1drt PCVClavaminate synthase 1 1.14.11.21 0.663
1qd1 FONFormimidoyltransferase-cyclodeaminase 2.1.2.5 0.660
3rye UNRFarnesyl pyrophosphate synthase 2.5.1.10 0.659
4nt0 3DUOrotidine 5'-phosphate decarboxylase 4.1.1.23 0.658
4fag GTQGentisate 1,2-dioxygenase / 0.655
4kyh ZSTLactoylglutathione lyase 4.4.1.5 0.654
2r2n KYNKynurenine/alpha-aminoadipate aminotransferase, mitochondrial 2.6.1.39 0.652
1u4s BIHL-lactate dehydrogenase 1.1.1.27 0.651
3o5t ADPNitrogen regulatory protein P-II 1 / 0.651
1n38 U3HRNA-directed RNA polymerase lambda-3 2.7.7.48 0.650
3uwq U5POrotidine 5'-phosphate decarboxylase / 0.650