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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
4ptf DCP DNA polymerase epsilon catalytic subunit A 2.7.7.7

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 1.159
4fjj TTPDNA-directed DNA polymerase / 0.963
4m42 ATPDNA-directed DNA polymerase / 0.962
4fjm DCPDNA-directed DNA polymerase / 0.956
4fjl DGTDNA-directed DNA polymerase / 0.948
4dtx TTPDNA-directed DNA polymerase / 0.927
4dtp DGTDNA-directed DNA polymerase / 0.922
4dtj TTPDNA-directed DNA polymerase / 0.920
3ne6 DCPDNA-directed DNA polymerase / 0.910
4fk4 DGTDNA-directed DNA polymerase / 0.889
4m3t ATPDNA-directed DNA polymerase / 0.888
4fj5 DTPDNA-directed DNA polymerase / 0.883
3lzj CTPDNA-directed DNA polymerase / 0.871
4fjh DGTDNA-directed DNA polymerase / 0.869
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.856
3sup DCPDNA-directed DNA polymerase / 0.839
4dto DCPDNA-directed DNA polymerase / 0.829
4m3x ATPDNA-directed DNA polymerase / 0.808
4khy TTPDNA-directed DNA polymerase / 0.801
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 0.788
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.766
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.760
4dtm DCPDNA-directed DNA polymerase / 0.758
3g6x DGTDNA polymerase iota 2.7.7.7 0.746
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.744
3au2 DGTDNA polymerase beta family (X family) / 0.743
3q23 G2PVirion DNA-directed RNA polymerase / 0.731
4xj4 3ATCyclic GMP-AMP synthase / 0.713
2b51 UTPRNA editing complex protein MP57 / 0.702
2q66 ATPPoly(A) polymerase 2.7.7.19 0.691
2ikf UTPPoly(A) polymerase, putative / 0.690
4u03 GTPCyclic GMP-AMP synthase / 0.685
4xj3 GTPCyclic GMP-AMP synthase / 0.682
1kqd FMNOxygen-insensitive NAD(P)H nitroreductase / 0.674
2vp0 TTPDeoxynucleoside kinase / 0.674
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.673
4fvq ATPTyrosine-protein kinase JAK2 / 0.672
2ixk TDOdTDP-4-dehydrorhamnose 3,5-epimerase 5.1.3.13 0.669
4k97 ATPCyclic GMP-AMP synthase / 0.669
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.666
2o4g TMPThree-prime repair exonuclease 1 3.1.11.2 0.666
3w3z GTPGTP-binding nuclear protein Ran / 0.665
4idn GNPAtlastin-1 3.6.5 0.663
5a2w AGSMitochondrial poly(A) polymerase / 0.663
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.661
3tw6 ADPPyruvate carboxylase / 0.661
1mmg AGSMyosin-2 heavy chain / 0.659
2jcs TTPDeoxynucleoside kinase / 0.659
1svm ATPLarge T antigen 3.6.4 0.657
3tkl GTPRas-related protein Rab-1A / 0.656
4idp GNPAtlastin-1 3.6.5 0.656
1r89 CTPCCA-adding enzyme 2.7.7.72 0.655
4ol0 GTPGTP-binding nuclear protein Ran / 0.654
3hiy UTPUncharacterized protein / 0.652
4u0m GTPCyclic GMP-AMP synthase / 0.652
4kvg GTPRas-related protein Rap-1A / 0.651
3zoz ADPPhosphoglycerate kinase 1 2.7.2.3 0.650