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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
4khy TTP DNA-directed DNA polymerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4khy TTPDNA-directed DNA polymerase / 1.078
4fj5 DTPDNA-directed DNA polymerase / 1.036
4fjj TTPDNA-directed DNA polymerase / 1.034
4m42 ATPDNA-directed DNA polymerase / 1.025
4dtp DGTDNA-directed DNA polymerase / 1.022
4fjl DGTDNA-directed DNA polymerase / 1.022
4fk4 DGTDNA-directed DNA polymerase / 1.006
3sup DCPDNA-directed DNA polymerase / 0.996
4dtx TTPDNA-directed DNA polymerase / 0.990
4dtj TTPDNA-directed DNA polymerase / 0.987
4fjh DGTDNA-directed DNA polymerase / 0.982
3ne6 DCPDNA-directed DNA polymerase / 0.955
4fjm DCPDNA-directed DNA polymerase / 0.953
4m3t ATPDNA-directed DNA polymerase / 0.953
4m3x ATPDNA-directed DNA polymerase / 0.945
3lzj CTPDNA-directed DNA polymerase / 0.943
4dto DCPDNA-directed DNA polymerase / 0.883
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.843
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.828
4dtm DCPDNA-directed DNA polymerase / 0.828
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.801
3g6x DGTDNA polymerase iota 2.7.7.7 0.781
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.771
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 0.767
3au2 DGTDNA polymerase beta family (X family) / 0.761
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.733
3q23 G2PVirion DNA-directed RNA polymerase / 0.726
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.722
2q66 ATPPoly(A) polymerase 2.7.7.19 0.716
3t3f N5PDNA polymerase I, thermostable 2.7.7.7 0.713
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.694
1r8c UTPCCA-adding enzyme 2.7.7.72 0.688
2q0f UTPPoly(A) polymerase, putative / 0.684
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.675
1jgt APCCarboxyethyl-arginine beta-lactam-synthase 6.3.3.4 0.673
1a2b GSPTransforming protein RhoA / 0.671
2q16 ITTdITP/XTP pyrophosphatase / 0.671
1p3j AP5Adenylate kinase / 0.666
4xj3 GTPCyclic GMP-AMP synthase / 0.665
2q0c CTPPoly(A) polymerase, putative / 0.664
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.664
3mhy ATPNitrogen regulatory protein P-II 1 / 0.663
4qnr ATPPsp operon transcriptional activator / 0.661
1r89 CTPCCA-adding enzyme 2.7.7.72 0.658
5dac AGSUncharacterized protein / 0.658
1n75 ATPGlutamate--tRNA ligase 6.1.1.17 0.656
2nom DUTPoly(A) polymerase, putative / 0.655
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.655
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.652
3myk ANPMyosin-2 heavy chain / 0.652
4xj4 3ATCyclic GMP-AMP synthase / 0.652
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.651
1eqg IBPProstaglandin G/H synthase 1 1.14.99.1 0.650