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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
3sup DCP DNA-directed DNA polymerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3sup DCPDNA-directed DNA polymerase / 1.161
3ne6 DCPDNA-directed DNA polymerase / 1.137
4dtp DGTDNA-directed DNA polymerase / 1.101
4dtj TTPDNA-directed DNA polymerase / 1.095
4fj5 DTPDNA-directed DNA polymerase / 1.075
3lzj CTPDNA-directed DNA polymerase / 1.066
4fjj TTPDNA-directed DNA polymerase / 1.064
4fjh DGTDNA-directed DNA polymerase / 1.056
4dtx TTPDNA-directed DNA polymerase / 1.054
4m42 ATPDNA-directed DNA polymerase / 1.046
4fk4 DGTDNA-directed DNA polymerase / 1.035
4fjl DGTDNA-directed DNA polymerase / 1.030
4fjm DCPDNA-directed DNA polymerase / 1.027
4dto DCPDNA-directed DNA polymerase / 1.019
4khy TTPDNA-directed DNA polymerase / 0.996
4m3t ATPDNA-directed DNA polymerase / 0.994
4m3x ATPDNA-directed DNA polymerase / 0.967
4dtm DCPDNA-directed DNA polymerase / 0.928
3g6x DGTDNA polymerase iota 2.7.7.7 0.862
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.840
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.839
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.795
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 0.757
2q66 ATPPoly(A) polymerase 2.7.7.19 0.755
3au2 DGTDNA polymerase beta family (X family) / 0.750
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.749
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.742
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.735
3t3f N5PDNA polymerase I, thermostable 2.7.7.7 0.730
3q23 G2PVirion DNA-directed RNA polymerase / 0.722
4kgk GTPUncharacterized protein / 0.696
3ova APCCCA-adding enzyme 2.7.7.72 0.680
1r89 CTPCCA-adding enzyme 2.7.7.72 0.677
4xj4 3ATCyclic GMP-AMP synthase / 0.675
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.673
5a2w AGSMitochondrial poly(A) polymerase / 0.672
4xj3 GTPCyclic GMP-AMP synthase / 0.671
1r8b ATPCCA-adding enzyme 2.7.7.72 0.669
2jlr ANPGenome polyprotein 3.4.21.91 0.667
3g8c ADPBiotin carboxylase 6.3.4.14 0.666
4xoi GTPTransforming protein RhoA / 0.664
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.662
3akl ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.659
3hiy UTPUncharacterized protein / 0.659
3tw6 ADPPyruvate carboxylase / 0.658
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.656
1gwn GTPRho-related GTP-binding protein RhoE / 0.655
1wdt GTPElongation factor G (EF-G-2) / 0.655
4k97 ATPCyclic GMP-AMP synthase / 0.654
2b51 UTPRNA editing complex protein MP57 / 0.653
3otb DGTProbable tRNA(His) guanylyltransferase 2.7.7.79 0.652
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.652
1m7b GTPRho-related GTP-binding protein RhoE / 0.651
1r8c UTPCCA-adding enzyme 2.7.7.72 0.651
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.650
3rv4 ADPBiotin carboxylase 6.3.4.14 0.650
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.650