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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
4df8 0L4 DNA polymerase I, thermostable 2.7.7.7

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 1.292
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 1.136
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 1.054
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.929
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.908
4dtj TTPDNA-directed DNA polymerase / 0.840
4dtx TTPDNA-directed DNA polymerase / 0.827
4m42 ATPDNA-directed DNA polymerase / 0.821
4m3t ATPDNA-directed DNA polymerase / 0.809
3t3f N5PDNA polymerase I, thermostable 2.7.7.7 0.802
4m3x ATPDNA-directed DNA polymerase / 0.798
4fjj TTPDNA-directed DNA polymerase / 0.796
4fj5 DTPDNA-directed DNA polymerase / 0.795
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.790
3ne6 DCPDNA-directed DNA polymerase / 0.779
4fk4 DGTDNA-directed DNA polymerase / 0.774
4khy TTPDNA-directed DNA polymerase / 0.767
3lzj CTPDNA-directed DNA polymerase / 0.763
3sup DCPDNA-directed DNA polymerase / 0.757
4fjl DGTDNA-directed DNA polymerase / 0.755
1qss DG3DNA polymerase I, thermostable 2.7.7.7 0.748
4dtp DGTDNA-directed DNA polymerase / 0.747
4dtm DCPDNA-directed DNA polymerase / 0.742
4fjm DCPDNA-directed DNA polymerase / 0.737
4fjh DGTDNA-directed DNA polymerase / 0.733
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.726
2q66 ATPPoly(A) polymerase 2.7.7.19 0.700
3hiy UTPUncharacterized protein / 0.698
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.693
2b56 UTPRNA editing complex protein MP57 / 0.692
4xj4 3ATCyclic GMP-AMP synthase / 0.689
2b51 UTPRNA editing complex protein MP57 / 0.686
2q0d ATPPoly(A) polymerase, putative / 0.686
4db1 ANPMyosin-7 / 0.686
4fvr ATPTyrosine-protein kinase JAK2 / 0.686
2xka GSPCell division protein FtsZ / 0.680
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.678
4fhp UTPTerminal uridylyltransferase cid1 / 0.672
3q23 G2PVirion DNA-directed RNA polymerase / 0.669
3law GNPRas-related protein Rab-7a / 0.668
2q16 ITTdITP/XTP pyrophosphatase / 0.665
3sl2 ATPSensor histidine kinase WalK / 0.665
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.665
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.663
4zol GTPTubulin alpha-1B chain / 0.660
1r8c UTPCCA-adding enzyme 2.7.7.72 0.658
2cls GTPRho-related GTP-binding protein Rho6 / 0.658
4k97 ATPCyclic GMP-AMP synthase / 0.657
3g6x DGTDNA polymerase iota 2.7.7.7 0.656
4dto DCPDNA-directed DNA polymerase / 0.656
5la6 GTPTubulin alpha-1B chain / 0.656
4u03 GTPCyclic GMP-AMP synthase / 0.652
2plm SIB5-methylthioadenosine/S-adenosylhomocysteine deaminase 3.5.4.28 0.651
4kgm ATPUncharacterized protein / 0.651
2j6x FMNLactate oxidase / 0.650