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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
2cvx 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
2cvx DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.990
3s87 DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.979
3k8t DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.976
3s8a DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.956
2wgh DTPRibonucleoside-diphosphate reductase large subunit 1.17.4.1 0.927
3tb9 ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.910
2cvv ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.909
3o0o TTPVitamin B12-dependent ribonucleotide reductase / 0.906
1xje TTPVitamin B12-dependent ribonucleotide reductase / 0.897
1xjj DGTVitamin B12-dependent ribonucleotide reductase / 0.896
3o0n TTPVitamin B12-dependent ribonucleotide reductase / 0.879
2cvu ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.854
2eud ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.850
1xjk DGTVitamin B12-dependent ribonucleotide reductase / 0.841
3s8c ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.829
2cvy TTPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.803
1peq TTPRibonucleoside-diphosphate reductase 2 subunit alpha 1.17.4.1 0.798
1xjg DTPVitamin B12-dependent ribonucleotide reductase / 0.752
1peo DCPRibonucleoside-diphosphate reductase 2 subunit alpha 1.17.4.1 0.731
4fkx CDPNucleoside diphosphate kinase / 0.704
3o0q TTPVitamin B12-dependent ribonucleotide reductase / 0.703
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.697
3rsr N5PRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.688
3ryh GTPTubulin alpha chain / 0.686
3oab DSTGeranyl diphosphate synthase large subunit / 0.685
3zcb ATPAdenosine monophosphate-protein transferase VbhT 2.7.7.n1 0.683
3zlm ANPAdenosine monophosphate-protein transferase NmFic 2.7.7.n1 0.682
3mvw BHZNickel-binding periplasmic protein / 0.681
3mw0 BHRNickel-binding periplasmic protein / 0.679
4dwb 0M7Farnesyl pyrophosphate synthase / 0.679
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.678
3krf DSTGeranyl diphosphate synthase large subunit / 0.678
4u0s ADPAdenosine monophosphate-protein transferase FICD 2.7.7.n1 0.677
2cvw TTPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.674
2r1r TTPRibonucleoside-diphosphate reductase 1 subunit alpha 1.17.4.1 0.674
4qm6 GTPMetallophosphoesterase / 0.673
4nu0 AP5Adenylate kinase / 0.672
1rqj RISFarnesyl diphosphate synthase 2.5.1.10 0.671
4ga3 4GAFarnesyl pyrophosphate synthase 2.5.1.10 0.669
4yj2 GTPTubulin alpha-1B chain / 0.667
5im3 DTPRibonucleoside-diphosphate reductase / 0.664
3mhy ATPNitrogen regulatory protein P-II 1 / 0.663
3mz9 BHNNickel-binding periplasmic protein / 0.663
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.658
4tv9 GTPTubulin alpha-1B chain / 0.656
3dkv AP5Adenylate kinase / 0.655
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.655
4iij GTPTubulin alpha-1B chain / 0.654
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.653
4q23 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.653
3lzw NAPFerredoxin--NADP reductase 2 1.18.1.2 0.652
4dxj 0M9Farnesyl pyrophosphate synthase / 0.652
1mez GDPAdenylosuccinate synthetase isozyme 1 / 0.651
1opm IYGPeptidyl-glycine alpha-amidating monooxygenase 1.14.17.3 0.651
2eg8 FOTDihydroorotase 3.5.2.3 0.651
2oo7 AP5Adenylate kinase / 0.651
4fvr ATPTyrosine-protein kinase JAK2 / 0.651
4yao 2AMNADPH--cytochrome P450 reductase / 0.651
2xul ATPNitrogen regulatory protein P-II / 0.650