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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
3ckt YDP Gag-Pol polyprotein 3.4.23.16

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3ckt YDPGag-Pol polyprotein 3.4.23.16 1.316
2qnn QN1Gag-Pol polyprotein 3.4.23.16 0.967
2r3t G4GGag-Pol polyprotein 3.4.23.16 0.941
3qpj N4IGag-Pol polyprotein 3.4.23.16 0.904
2pwr G4GGag-Pol polyprotein 3.4.23.16 0.897
3qrm NK7Gag-Pol polyprotein 3.4.23.16 0.891
2r43 G3GGag-Pol polyprotein 3.4.23.16 0.871
2pwc G3GGag-Pol polyprotein 3.4.23.16 0.865
3qrs NK8Gag-Pol polyprotein 3.4.23.16 0.860
2qnq QN3Gag-Pol polyprotein 3.4.23.16 0.856
3qbf JHGGag-Pol polyprotein 3.4.23.16 0.850
2r3w G3GGag-Pol polyprotein 3.4.23.16 0.825
2qnp QN2Gag-Pol polyprotein 3.4.23.16 0.820
2r38 G4GGag-Pol polyprotein 3.4.23.16 0.817
2pqz G0GGag-Pol polyprotein 3.4.23.16 0.786
1odx 0E8Gag-Pol polyprotein 3.4.23.16 0.764
3qih NI7Gag-Pol polyprotein 3.4.23.16 0.751
1odw 0E8Gag-Pol polyprotein 3.4.23.16 0.735
4djp M73Pol polyprotein / 0.718
4gb2 0LQGag-Pol polyprotein 2.7.7.49 0.709
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.705
3bgc LJHGag-Pol polyprotein 3.4.23.16 0.704
1mtr PI6Gag-Pol polyprotein 3.4.23.16 0.684
3sa7 55AProtease / 0.683
1b6p PI7Gag-Pol polyprotein 3.4.23.16 0.676
3qro NK9Gag-Pol polyprotein 3.4.23.16 0.674
3a2o KNJGag-Pol polyprotein 3.4.23.16 0.672
3bgb LJGGag-Pol polyprotein 3.4.23.16 0.671
1ebw BEIGag-Pol polyprotein 3.4.23.16 0.668
1zsr 0ZTGag-Pol polyprotein 3.4.23.16 0.668
1d4k PI8Gag-Pol polyprotein 3.4.23.16 0.665
3ufl 508Beta-secretase 1 3.4.23.46 0.663
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.662
1ebz BECGag-Pol polyprotein 3.4.23.16 0.657
2i4v DJRV-1 protease / 0.655
1hxw RITGag-Pol polyprotein / 0.654
2fdd 385Pol protein / 0.654
3o99 K13Pol polyprotein / 0.654
1msm JE2Gag-Pol polyprotein 3.4.23.16 0.652