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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
4dtm DCP DNA-directed DNA polymerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4dtm DCPDNA-directed DNA polymerase / 1.055
4dto DCPDNA-directed DNA polymerase / 0.991
3ne6 DCPDNA-directed DNA polymerase / 0.933
3sup DCPDNA-directed DNA polymerase / 0.928
4dtx TTPDNA-directed DNA polymerase / 0.925
4dtj TTPDNA-directed DNA polymerase / 0.918
4fjh DGTDNA-directed DNA polymerase / 0.903
4fjj TTPDNA-directed DNA polymerase / 0.884
4dtp DGTDNA-directed DNA polymerase / 0.881
3lzj CTPDNA-directed DNA polymerase / 0.873
4fj5 DTPDNA-directed DNA polymerase / 0.870
4fk4 DGTDNA-directed DNA polymerase / 0.865
4fjm DCPDNA-directed DNA polymerase / 0.854
4m3t ATPDNA-directed DNA polymerase / 0.853
4m3x ATPDNA-directed DNA polymerase / 0.851
4m42 ATPDNA-directed DNA polymerase / 0.851
4fjl DGTDNA-directed DNA polymerase / 0.846
4khy TTPDNA-directed DNA polymerase / 0.828
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.758
3g6x DGTDNA polymerase iota 2.7.7.7 0.748
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 0.742
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.732
3q23 G2PVirion DNA-directed RNA polymerase / 0.711
3au2 DGTDNA polymerase beta family (X family) / 0.698
1r8c UTPCCA-adding enzyme 2.7.7.72 0.684
5a30 AGSMitochondrial poly(A) polymerase / 0.682
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.679
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.671
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.668
3ftq GNPSeptin-2 / 0.664
3hiy UTPUncharacterized protein / 0.664
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.664
5a2w AGSMitochondrial poly(A) polymerase / 0.658
2b56 UTPRNA editing complex protein MP57 / 0.657
2ikf UTPPoly(A) polymerase, putative / 0.657
3t3f N5PDNA polymerase I, thermostable 2.7.7.7 0.656
1mb9 ATPCarboxyethyl-arginine beta-lactam-synthase 6.3.3.4 0.653
3fbc TYDNucleoside diphosphate kinase 2.7.4.6 0.653
3myk ANPMyosin-2 heavy chain / 0.651