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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
3ne6 DCP DNA-directed DNA polymerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3ne6 DCPDNA-directed DNA polymerase / 1.209
3sup DCPDNA-directed DNA polymerase / 1.137
4dtp DGTDNA-directed DNA polymerase / 1.132
4fj5 DTPDNA-directed DNA polymerase / 1.126
4fjj TTPDNA-directed DNA polymerase / 1.112
4dtx TTPDNA-directed DNA polymerase / 1.110
4fjh DGTDNA-directed DNA polymerase / 1.109
4dtj TTPDNA-directed DNA polymerase / 1.107
3lzj CTPDNA-directed DNA polymerase / 1.088
4m42 ATPDNA-directed DNA polymerase / 1.074
4fk4 DGTDNA-directed DNA polymerase / 1.070
4m3t ATPDNA-directed DNA polymerase / 1.068
4fjl DGTDNA-directed DNA polymerase / 1.060
4fjm DCPDNA-directed DNA polymerase / 1.048
4dto DCPDNA-directed DNA polymerase / 1.027
4m3x ATPDNA-directed DNA polymerase / 1.022
4khy TTPDNA-directed DNA polymerase / 0.955
4dtm DCPDNA-directed DNA polymerase / 0.933
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.910
3g6x DGTDNA polymerase iota 2.7.7.7 0.857
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.823
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.781
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.780
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 0.779
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.759
3au2 DGTDNA polymerase beta family (X family) / 0.758
3q23 G2PVirion DNA-directed RNA polymerase / 0.742
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.726
4xj4 3ATCyclic GMP-AMP synthase / 0.723
2q66 ATPPoly(A) polymerase 2.7.7.19 0.721
3t3f N5PDNA polymerase I, thermostable 2.7.7.7 0.713
1r8b ATPCCA-adding enzyme 2.7.7.72 0.699
4k97 ATPCyclic GMP-AMP synthase / 0.699
4u03 GTPCyclic GMP-AMP synthase / 0.699
1r89 CTPCCA-adding enzyme 2.7.7.72 0.695
1qss DG3DNA polymerase I, thermostable 2.7.7.7 0.691
1r8c UTPCCA-adding enzyme 2.7.7.72 0.681
3ftq GNPSeptin-2 / 0.681
4xj3 GTPCyclic GMP-AMP synthase / 0.681
2jlr ANPGenome polyprotein 3.4.21.91 0.668
1cjv DADAdenylate cyclase type 2 / 0.667
1cjv DADAdenylate cyclase type 5 / 0.667
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.666
1fcb FMNCytochrome b2, mitochondrial 1.1.2.3 0.662
2zru FMNIsopentenyl-diphosphate delta-isomerase / 0.662
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.661
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.661
3ova APCCCA-adding enzyme 2.7.7.72 0.661
2vp0 TTPDeoxynucleoside kinase / 0.660
3hiy UTPUncharacterized protein / 0.658
4kgk GTPUncharacterized protein / 0.658
5a2w AGSMitochondrial poly(A) polymerase / 0.653
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.652
1qd1 FONFormimidoyltransferase-cyclodeaminase 2.1.2.5 0.651
3g8c ADPBiotin carboxylase 6.3.4.14 0.651