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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
4m3t ATP DNA-directed DNA polymerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4m3t ATPDNA-directed DNA polymerase / 1.094
4dtx TTPDNA-directed DNA polymerase / 1.083
4m3x ATPDNA-directed DNA polymerase / 1.069
3ne6 DCPDNA-directed DNA polymerase / 1.068
4fjj TTPDNA-directed DNA polymerase / 1.068
4fj5 DTPDNA-directed DNA polymerase / 1.066
4fjh DGTDNA-directed DNA polymerase / 1.062
4fk4 DGTDNA-directed DNA polymerase / 1.051
4fjm DCPDNA-directed DNA polymerase / 1.048
4dtj TTPDNA-directed DNA polymerase / 1.046
3lzj CTPDNA-directed DNA polymerase / 1.042
4fjl DGTDNA-directed DNA polymerase / 1.036
4m42 ATPDNA-directed DNA polymerase / 1.010
4dtp DGTDNA-directed DNA polymerase / 0.997
3sup DCPDNA-directed DNA polymerase / 0.994
4khy TTPDNA-directed DNA polymerase / 0.953
4dto DCPDNA-directed DNA polymerase / 0.920
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.888
4dtm DCPDNA-directed DNA polymerase / 0.853
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 0.809
3g6x DGTDNA polymerase iota 2.7.7.7 0.807
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.786
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.752
3au2 DGTDNA polymerase beta family (X family) / 0.738
3q23 G2PVirion DNA-directed RNA polymerase / 0.725
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.707
1cjv DADAdenylate cyclase type 2 / 0.706
1cjv DADAdenylate cyclase type 5 / 0.706
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.703
1r8b ATPCCA-adding enzyme 2.7.7.72 0.687
2q66 ATPPoly(A) polymerase 2.7.7.19 0.687
1r8c UTPCCA-adding enzyme 2.7.7.72 0.685
1oe0 TTPDeoxynucleoside kinase / 0.683
1r89 CTPCCA-adding enzyme 2.7.7.72 0.683
4xj4 3ATCyclic GMP-AMP synthase / 0.683
3hiy UTPUncharacterized protein / 0.675
3vhx GTPADP-ribosylation factor 6 / 0.675
4u03 GTPCyclic GMP-AMP synthase / 0.675
2b56 UTPRNA editing complex protein MP57 / 0.673
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.672
1n75 ATPGlutamate--tRNA ligase 6.1.1.17 0.671
5a2w AGSMitochondrial poly(A) polymerase / 0.671
2b51 UTPRNA editing complex protein MP57 / 0.666
4xj3 GTPCyclic GMP-AMP synthase / 0.664
4fvr ATPTyrosine-protein kinase JAK2 / 0.663
2jlr ANPGenome polyprotein 3.4.21.91 0.660
3t3f N5PDNA polymerase I, thermostable 2.7.7.7 0.660
2jcs TTPDeoxynucleoside kinase / 0.657
1xs4 DCPdCTP deaminase / 0.655
4tnr DTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.654
3q8x UD1Toxin zeta / 0.653
4fvq ATPTyrosine-protein kinase JAK2 / 0.651
4lt6 3ATPoly(A) polymerase gamma 2.7.7.19 0.650