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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
3t3f N5P DNA polymerase I, thermostable 2.7.7.7

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3t3f N5PDNA polymerase I, thermostable 2.7.7.7 1.111
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.826
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 0.802
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.784
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.767
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.757
3sup DCPDNA-directed DNA polymerase / 0.730
4dtj TTPDNA-directed DNA polymerase / 0.727
3ne6 DCPDNA-directed DNA polymerase / 0.713
4khy TTPDNA-directed DNA polymerase / 0.713
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.709
4dtp DGTDNA-directed DNA polymerase / 0.708
4fk4 DGTDNA-directed DNA polymerase / 0.699
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.690
3hiy UTPUncharacterized protein / 0.689
4m42 ATPDNA-directed DNA polymerase / 0.681
3ftq GNPSeptin-2 / 0.670
4jsy GTPMetallophosphoesterase / 0.668
4dtx TTPDNA-directed DNA polymerase / 0.667
4fjh DGTDNA-directed DNA polymerase / 0.666
1n6l GTPRas-related protein Rab-5A / 0.665
2b51 UTPRNA editing complex protein MP57 / 0.663
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.662
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.662
2x0q ATPAlcaligin biosynthesis protein / 0.661
4fj5 DTPDNA-directed DNA polymerase / 0.660
4m3t ATPDNA-directed DNA polymerase / 0.660
3law GNPRas-related protein Rab-7a / 0.659
4ovi N01Phenylacetone monooxygenase 1.14.13.92 0.659
1f5n GNPGuanylate-binding protein 1 / 0.657
1jgt APCCarboxyethyl-arginine beta-lactam-synthase 6.3.3.4 0.657
2bku GTPGTP-binding nuclear protein Ran / 0.657
5i4n ATPTyrosine-protein kinase JAK2 / 0.657
1gwn GTPRho-related GTP-binding protein RhoE / 0.656
2ikf UTPPoly(A) polymerase, putative / 0.656
4dtm DCPDNA-directed DNA polymerase / 0.656
1fmw ATPMyosin-2 heavy chain / 0.655
3b1x GNPFerrous iron transport protein B / 0.655
3krf DSTGeranyl diphosphate synthase large subunit / 0.655
3qbt GNPRas-related protein Rab-8A / 0.655
3tkl GTPRas-related protein Rab-1A / 0.655
4dvg GSPRho family GTPase / 0.655
2uz3 TTPThymidine kinase / 0.654
1t91 GTPRas-related protein Rab-7a / 0.653
2q16 ITTdITP/XTP pyrophosphatase / 0.653
3kz1 GSPTransforming protein RhoA / 0.653
4tnp DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.653
1w5t ANPORC1-type DNA replication protein 2 / 0.652
1ky2 GNPGTP-binding protein YPT7 / 0.651
2cl6 CAGGTPase HRas / 0.651
4lhw GNPRas-related protein Rab-8A / 0.651
5bn3 ADPV-type ATP synthase alpha chain / 0.651
5bn3 ADPNEQ263 / 0.651
3m0e ATPTranscriptional regulator (NtrC family) / 0.650