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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
3k8t DGT Ribonucleoside-diphosphate reductase large chain 1 1.17.4.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3k8t DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 1.006
2cvx DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.976
3s87 DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.959
1xjj DGTVitamin B12-dependent ribonucleotide reductase / 0.918
3o0o TTPVitamin B12-dependent ribonucleotide reductase / 0.914
1xje TTPVitamin B12-dependent ribonucleotide reductase / 0.911
2wgh DTPRibonucleoside-diphosphate reductase large subunit 1.17.4.1 0.908
3s8a DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.891
3tb9 ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.882
1xjk DGTVitamin B12-dependent ribonucleotide reductase / 0.880
3o0n TTPVitamin B12-dependent ribonucleotide reductase / 0.861
2cvv ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.851
1peq TTPRibonucleoside-diphosphate reductase 2 subunit alpha 1.17.4.1 0.830
2cvu ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.819
2cvy TTPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.805
1xjg DTPVitamin B12-dependent ribonucleotide reductase / 0.787
2eud ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.756
1peo DCPRibonucleoside-diphosphate reductase 2 subunit alpha 1.17.4.1 0.739
3rsr N5PRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.720
3o0q TTPVitamin B12-dependent ribonucleotide reductase / 0.719
2cvw TTPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.703
3s8c ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.699
3zcb ATPAdenosine monophosphate-protein transferase VbhT 2.7.7.n1 0.698
5im3 DTPRibonucleoside-diphosphate reductase / 0.685
3mvw BHZNickel-binding periplasmic protein / 0.680
3mw0 BHRNickel-binding periplasmic protein / 0.678
2r1r TTPRibonucleoside-diphosphate reductase 1 subunit alpha 1.17.4.1 0.676
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.676
3zlm ANPAdenosine monophosphate-protein transferase NmFic 2.7.7.n1 0.674
1u5a BIKL-lactate dehydrogenase 1.1.1.27 0.667
3se5 ANPAdenosine monophosphate-protein transferase NmFic 2.7.7.n1 0.663
3lzw NAPFerredoxin--NADP reductase 2 1.18.1.2 0.661
3krf DSTGeranyl diphosphate synthase large subunit / 0.659
1xjn DTPVitamin B12-dependent ribonucleotide reductase / 0.658
4iij GTPTubulin alpha-1B chain / 0.658
5i4n ATPTyrosine-protein kinase JAK2 / 0.657
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.656
1lot ATPActin, alpha skeletal muscle / 0.653
4qm6 GTPMetallophosphoesterase / 0.650