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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
3g6x DGT DNA polymerase iota 2.7.7.7

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3g6x DGTDNA polymerase iota 2.7.7.7 1.190
4fjm DCPDNA-directed DNA polymerase / 0.905
4m42 ATPDNA-directed DNA polymerase / 0.881
4dtp DGTDNA-directed DNA polymerase / 0.872
3sup DCPDNA-directed DNA polymerase / 0.862
3lzj CTPDNA-directed DNA polymerase / 0.861
4fj5 DTPDNA-directed DNA polymerase / 0.858
3ne6 DCPDNA-directed DNA polymerase / 0.857
4dtj TTPDNA-directed DNA polymerase / 0.856
4fjh DGTDNA-directed DNA polymerase / 0.832
4fk4 DGTDNA-directed DNA polymerase / 0.828
4m3x ATPDNA-directed DNA polymerase / 0.825
4dtx TTPDNA-directed DNA polymerase / 0.821
4fjl DGTDNA-directed DNA polymerase / 0.819
4fjj TTPDNA-directed DNA polymerase / 0.818
4dto DCPDNA-directed DNA polymerase / 0.811
4m3t ATPDNA-directed DNA polymerase / 0.807
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.782
4khy TTPDNA-directed DNA polymerase / 0.781
3au2 DGTDNA polymerase beta family (X family) / 0.750
4dtm DCPDNA-directed DNA polymerase / 0.748
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.746
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.745
3q23 G2PVirion DNA-directed RNA polymerase / 0.738
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.737
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.733
2b56 UTPRNA editing complex protein MP57 / 0.718
4xj4 3ATCyclic GMP-AMP synthase / 0.716
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.714
4u03 GTPCyclic GMP-AMP synthase / 0.706
4k97 ATPCyclic GMP-AMP synthase / 0.700
3er9 3ATPoly(A) polymerase catalytic subunit 2.7.7.19 0.699
3hiy UTPUncharacterized protein / 0.696
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.694
4qnr ATPPsp operon transcriptional activator / 0.688
2q0d ATPPoly(A) polymerase, putative / 0.686
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.685
2q66 ATPPoly(A) polymerase 2.7.7.19 0.685
1cjv DADAdenylate cyclase type 2 / 0.684
1cjv DADAdenylate cyclase type 5 / 0.684
4yvz 3ATDNA integrity scanning protein DisA / 0.682
1kqc FMNOxygen-insensitive NAD(P)H nitroreductase / 0.681
1ylr FMNOxygen-insensitive NAD(P)H nitroreductase / 0.681
1kqd FMNOxygen-insensitive NAD(P)H nitroreductase / 0.680
2q0c CTPPoly(A) polymerase, putative / 0.680
1kqb FMNOxygen-insensitive NAD(P)H nitroreductase / 0.679
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.678
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.675
2jlr ANPGenome polyprotein 3.4.21.91 0.674
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.672
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.671
1ooq FMNOxygen-insensitive NAD(P)H nitroreductase / 0.671
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.670
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.669
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.669
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.669
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.668
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.665
5a2w AGSMitochondrial poly(A) polymerase / 0.665
3m0e ATPTranscriptional regulator (NtrC family) / 0.664
4at8 ATPInterleukin enhancer-binding factor 2 / 0.662
1r8c UTPCCA-adding enzyme 2.7.7.72 0.661
4lrw GDPGTPase KRas / 0.661
3n0z 3ATAdenylate cyclase 2 / 0.658
3wbz ATPtRNA(His) guanylyltransferase {ECO:0000256|PIRNR:PIRNR028980} / 0.658
4kgm ATPUncharacterized protein / 0.658
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.656
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 0.656
3ll9 ADPIsopentenyl phosphate kinase / 0.655
4qm6 GTPMetallophosphoesterase / 0.655
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.654
2ikf UTPPoly(A) polymerase, putative / 0.654
4o25 GTPGTP-binding protein Rheb / 0.654
1oe0 TTPDeoxynucleoside kinase / 0.653
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.653
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.652
2b51 UTPRNA editing complex protein MP57 / 0.652
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.652
2rgx AP5Adenylate kinase / 0.652
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.651
1gox FMNPeroxisomal (S)-2-hydroxy-acid oxidase 1.1.3.15 0.650
4txz G2PCyclic GMP-AMP synthase / 0.650