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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
1qtm TTP DNA polymerase I, thermostable 2.7.7.7

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 1.109
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.992
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 0.908
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.869
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.858
1qss DG3DNA polymerase I, thermostable 2.7.7.7 0.795
3ne6 DCPDNA-directed DNA polymerase / 0.780
4m42 ATPDNA-directed DNA polymerase / 0.769
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.766
3t3f N5PDNA polymerase I, thermostable 2.7.7.7 0.757
3sup DCPDNA-directed DNA polymerase / 0.742
4dtp DGTDNA-directed DNA polymerase / 0.740
3lzj CTPDNA-directed DNA polymerase / 0.739
4fj5 DTPDNA-directed DNA polymerase / 0.737
4khy TTPDNA-directed DNA polymerase / 0.733
4dtj TTPDNA-directed DNA polymerase / 0.732
4fk4 DGTDNA-directed DNA polymerase / 0.729
4fjj TTPDNA-directed DNA polymerase / 0.718
3g6x DGTDNA polymerase iota 2.7.7.7 0.714
4fjm DCPDNA-directed DNA polymerase / 0.714
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.710
4fjl DGTDNA-directed DNA polymerase / 0.704
4fjh DGTDNA-directed DNA polymerase / 0.703
4m3t ATPDNA-directed DNA polymerase / 0.703
1cjv DADAdenylate cyclase type 2 / 0.701
1cjv DADAdenylate cyclase type 5 / 0.701
4m3x ATPDNA-directed DNA polymerase / 0.694
4dtx TTPDNA-directed DNA polymerase / 0.691
2ikf UTPPoly(A) polymerase, putative / 0.677
2q66 ATPPoly(A) polymerase 2.7.7.19 0.674
2b51 UTPRNA editing complex protein MP57 / 0.670
3wbz ATPtRNA(His) guanylyltransferase {ECO:0000256|PIRNR:PIRNR028980} / 0.665
3au2 DGTDNA polymerase beta family (X family) / 0.661
5a2w AGSMitochondrial poly(A) polymerase / 0.661
4xj4 3ATCyclic GMP-AMP synthase / 0.658
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.657
4fvq ATPTyrosine-protein kinase JAK2 / 0.656
1mmg AGSMyosin-2 heavy chain / 0.652
4dto DCPDNA-directed DNA polymerase / 0.652
4pkg ATPActin, alpha skeletal muscle / 0.652
3q9l ATPSeptum site-determining protein MinD / 0.650