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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
4fk4 DGT DNA-directed DNA polymerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4fk4 DGTDNA-directed DNA polymerase / 1.111
4fj5 DTPDNA-directed DNA polymerase / 1.101
4fjj TTPDNA-directed DNA polymerase / 1.101
4fjh DGTDNA-directed DNA polymerase / 1.097
4fjl DGTDNA-directed DNA polymerase / 1.091
4dtj TTPDNA-directed DNA polymerase / 1.088
4fjm DCPDNA-directed DNA polymerase / 1.078
4m42 ATPDNA-directed DNA polymerase / 1.072
3ne6 DCPDNA-directed DNA polymerase / 1.070
4m3x ATPDNA-directed DNA polymerase / 1.069
4dtx TTPDNA-directed DNA polymerase / 1.052
4m3t ATPDNA-directed DNA polymerase / 1.051
3lzj CTPDNA-directed DNA polymerase / 1.041
4dtp DGTDNA-directed DNA polymerase / 1.038
3sup DCPDNA-directed DNA polymerase / 1.035
4khy TTPDNA-directed DNA polymerase / 1.006
4dto DCPDNA-directed DNA polymerase / 0.901
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.889
4dtm DCPDNA-directed DNA polymerase / 0.865
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.845
3g6x DGTDNA polymerase iota 2.7.7.7 0.828
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 0.774
3q23 G2PVirion DNA-directed RNA polymerase / 0.766
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.758
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.750
3au2 DGTDNA polymerase beta family (X family) / 0.744
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.742
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.729
2q66 ATPPoly(A) polymerase 2.7.7.19 0.723
1cjv DADAdenylate cyclase type 2 / 0.722
1cjv DADAdenylate cyclase type 5 / 0.722
4xj4 3ATCyclic GMP-AMP synthase / 0.708
3t3f N5PDNA polymerase I, thermostable 2.7.7.7 0.699
1r89 CTPCCA-adding enzyme 2.7.7.72 0.695
2b56 UTPRNA editing complex protein MP57 / 0.689
4u03 GTPCyclic GMP-AMP synthase / 0.689
1r8b ATPCCA-adding enzyme 2.7.7.72 0.688
1r8c UTPCCA-adding enzyme 2.7.7.72 0.686
4k97 ATPCyclic GMP-AMP synthase / 0.672
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.672
2jcs TTPDeoxynucleoside kinase / 0.663
5a2w AGSMitochondrial poly(A) polymerase / 0.661
2q16 ITTdITP/XTP pyrophosphatase / 0.659
3myk ANPMyosin-2 heavy chain / 0.653
4qm6 GTPMetallophosphoesterase / 0.653
1n75 ATPGlutamate--tRNA ligase 6.1.1.17 0.652
4fvq ATPTyrosine-protein kinase JAK2 / 0.651
4j36 1HRKynurenine 3-monooxygenase / 0.651
4kgk GTPUncharacterized protein / 0.650