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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
1xjk DGT Vitamin B12-dependent ribonucleotide reductase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1xjk DGTVitamin B12-dependent ribonucleotide reductase / 1.189
1xjj DGTVitamin B12-dependent ribonucleotide reductase / 1.088
3o0o TTPVitamin B12-dependent ribonucleotide reductase / 0.947
1xje TTPVitamin B12-dependent ribonucleotide reductase / 0.908
3o0q TTPVitamin B12-dependent ribonucleotide reductase / 0.906
3o0n TTPVitamin B12-dependent ribonucleotide reductase / 0.886
3k8t DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.880
2wgh DTPRibonucleoside-diphosphate reductase large subunit 1.17.4.1 0.863
3tb9 ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.854
2cvx DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.841
3s87 DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.825
1peq TTPRibonucleoside-diphosphate reductase 2 subunit alpha 1.17.4.1 0.797
1xjn DTPVitamin B12-dependent ribonucleotide reductase / 0.795
2cvu ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.794
2cvv ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.793
1xjg DTPVitamin B12-dependent ribonucleotide reductase / 0.764
3s8a DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.753
1peo DCPRibonucleoside-diphosphate reductase 2 subunit alpha 1.17.4.1 0.738
2cvy TTPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.701
3s8c ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.693
3rep ATPIntegrin-linked protein kinase 2.7.11.1 0.688
2o1o RISPutative farnesyl pyrophosphate synthase / 0.683
3kmw ATPIntegrin-linked protein kinase 2.7.11.1 0.680
2cvw TTPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.678
3oab DSTGeranyl diphosphate synthase large subunit / 0.678
2zxu DSTtRNA dimethylallyltransferase 2.5.1.75 0.670
2v9x DUTdCTP deaminase / 0.664
2eud ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.658
3ldw ZOLFarnesyl pyrophosphate synthase, putative / 0.657
1u7w CTPCoenzyme A biosynthesis bifunctional protein CoaBC 6.3.2.5 0.656
3vhx GTPADP-ribosylation factor 6 / 0.654
2wqp WQPPolysialic acid capsule biosynthesis protein SiaC / 0.652
4zse ANPEpidermal growth factor receptor 2.7.10.1 0.652
3krf DSTGeranyl diphosphate synthase large subunit / 0.651
4ipe ANPTNF receptor-associated protein 1 / 0.650
4nu0 AP5Adenylate kinase / 0.650