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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
4dto DCP DNA-directed DNA polymerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4dto DCPDNA-directed DNA polymerase / 1.076
3ne6 DCPDNA-directed DNA polymerase / 1.027
3sup DCPDNA-directed DNA polymerase / 1.019
4dtm DCPDNA-directed DNA polymerase / 0.991
4dtx TTPDNA-directed DNA polymerase / 0.963
4dtj TTPDNA-directed DNA polymerase / 0.961
4dtp DGTDNA-directed DNA polymerase / 0.955
3lzj CTPDNA-directed DNA polymerase / 0.942
4fj5 DTPDNA-directed DNA polymerase / 0.927
4m3t ATPDNA-directed DNA polymerase / 0.920
4fjj TTPDNA-directed DNA polymerase / 0.919
4fjh DGTDNA-directed DNA polymerase / 0.909
4m42 ATPDNA-directed DNA polymerase / 0.908
4fjm DCPDNA-directed DNA polymerase / 0.905
4fk4 DGTDNA-directed DNA polymerase / 0.901
4khy TTPDNA-directed DNA polymerase / 0.883
4fjl DGTDNA-directed DNA polymerase / 0.881
4m3x ATPDNA-directed DNA polymerase / 0.864
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.829
3g6x DGTDNA polymerase iota 2.7.7.7 0.811
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.741
3q23 G2PVirion DNA-directed RNA polymerase / 0.729
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.729
3au2 DGTDNA polymerase beta family (X family) / 0.709
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.697
4k97 ATPCyclic GMP-AMP synthase / 0.695
2q66 ATPPoly(A) polymerase 2.7.7.19 0.690
5a30 AGSMitochondrial poly(A) polymerase / 0.678
4kgk GTPUncharacterized protein / 0.672
4u03 GTPCyclic GMP-AMP synthase / 0.669
2b51 UTPRNA editing complex protein MP57 / 0.660
3gwc FADFlavin-dependent thymidylate synthase 2.1.1.148 0.659
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.659
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.658
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 0.656
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.655
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.652
2x2r ADPKinesin-like protein KIF11 / 0.652
5cyo GDPSeptin-9 / 0.652
2bku GTPGTP-binding nuclear protein Ran / 0.650
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.650