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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
4df4 0L3 DNA polymerase I, thermostable 2.7.7.7

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 1.370
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 1.136
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.913
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.884
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.858
4dtp DGTDNA-directed DNA polymerase / 0.846
4khy TTPDNA-directed DNA polymerase / 0.843
3sup DCPDNA-directed DNA polymerase / 0.840
3t3f N5PDNA polymerase I, thermostable 2.7.7.7 0.826
4fj5 DTPDNA-directed DNA polymerase / 0.826
4m42 ATPDNA-directed DNA polymerase / 0.794
3lzj CTPDNA-directed DNA polymerase / 0.786
3g6x DGTDNA polymerase iota 2.7.7.7 0.782
3ne6 DCPDNA-directed DNA polymerase / 0.781
4dtj TTPDNA-directed DNA polymerase / 0.781
4fjj TTPDNA-directed DNA polymerase / 0.772
4dtx TTPDNA-directed DNA polymerase / 0.768
4fjl DGTDNA-directed DNA polymerase / 0.761
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.760
4m3t ATPDNA-directed DNA polymerase / 0.752
4fk4 DGTDNA-directed DNA polymerase / 0.750
4fjh DGTDNA-directed DNA polymerase / 0.746
4m3x ATPDNA-directed DNA polymerase / 0.731
4dto DCPDNA-directed DNA polymerase / 0.729
4fjm DCPDNA-directed DNA polymerase / 0.727
2q66 ATPPoly(A) polymerase 2.7.7.19 0.724
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.721
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.706
2b56 UTPRNA editing complex protein MP57 / 0.701
2b51 UTPRNA editing complex protein MP57 / 0.698
4jsy GTPMetallophosphoesterase / 0.692
4k97 ATPCyclic GMP-AMP synthase / 0.689
4rje FNRLactate oxidase / 0.687
1qss DG3DNA polymerase I, thermostable 2.7.7.7 0.682
4tnr DTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.682
4dtm DCPDNA-directed DNA polymerase / 0.679
3hiy UTPUncharacterized protein / 0.678
4yl2 FMNLactate oxidase / 0.677
2e77 FMNLactate oxidase / 0.676
4xj4 3ATCyclic GMP-AMP synthase / 0.676
2j9g ADPBiotin carboxylase 6.3.4.14 0.672
5drd ATPAurora kinase A 2.7.11.1 0.672
3tkl GTPRas-related protein Rab-1A / 0.667
2uz3 TTPThymidine kinase / 0.665
5a2w AGSMitochondrial poly(A) polymerase / 0.665
2nli FMNLactate oxidase / 0.664
2zxu DSTtRNA dimethylallyltransferase 2.5.1.75 0.664
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.662
2zfa FMNLactate oxidase / 0.660
3au2 DGTDNA polymerase beta family (X family) / 0.660
1t91 GTPRas-related protein Rab-7a / 0.658
3wbz ATPtRNA(His) guanylyltransferase {ECO:0000256|PIRNR:PIRNR028980} / 0.657
3wyf GTPGTP-binding nuclear protein / 0.657
4qm6 GTPMetallophosphoesterase / 0.656
4nyj GNPGTPase HRas / 0.655
4u03 GTPCyclic GMP-AMP synthase / 0.655
4db1 ANPMyosin-7 / 0.654
4z54 GDPNeuronal-specific septin-3 / 0.653