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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
3duy AFJ Beta-secretase 1 3.4.23.46

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3duy AFJBeta-secretase 1 3.4.23.46 1.282
3k5d XLIBeta-secretase 1 3.4.23.46 1.150
3dv1 AR9Beta-secretase 1 3.4.23.46 1.057
2g94 ZPQBeta-secretase 1 3.4.23.46 0.996
2f3e AXQBeta-secretase 1 3.4.23.46 0.991
2p4j 23IBeta-secretase 1 3.4.23.46 0.913
3k5f AYHBeta-secretase 1 3.4.23.46 0.909
2f3f AXFBeta-secretase 1 3.4.23.46 0.879
3ixk 929Beta-secretase 1 3.4.23.46 0.808
3ixj 586Beta-secretase 1 3.4.23.46 0.806
3i25 MV7Beta-secretase 1 3.4.23.46 0.792
2fdp FRPBeta-secretase 1 3.4.23.46 0.779
1qrp HH0Pepsin A-4 3.4.23.1 0.777
1eag A70Candidapepsin-2 3.4.23.24 0.746
3k5g BJCBeta-secretase 1 3.4.23.46 0.742
3cib 314Beta-secretase 1 3.4.23.46 0.741
1ppm 0P1Penicillopepsin-1 3.4.23.20 0.739
3dm6 757Beta-secretase 1 3.4.23.46 0.739
1ppl 1Z7Penicillopepsin-1 3.4.23.20 0.736
3cid 318Beta-secretase 1 3.4.23.46 0.735
2jjj 0QSEndothiapepsin 3.4.23.22 0.734
2iqg F2IBeta-secretase 1 3.4.23.46 0.730
2xfk AA9Beta-secretase 1 3.4.23.46 0.729
2b8v 3BNBeta-secretase 1 3.4.23.46 0.723
1rne C60Renin 3.4.23.15 0.722
3lpj Z75Beta-secretase 1 3.4.23.46 0.720
1gvv 0GMEndothiapepsin 3.4.23.22 0.718
2vj6 VG5Beta-secretase 1 3.4.23.46 0.715
4fco 0U4Beta-secretase 1 3.4.23.46 0.715
1bxq PP8Penicillopepsin-1 3.4.23.20 0.712
2hiz LIJBeta-secretase 1 3.4.23.46 0.711
2viy VG3Beta-secretase 1 3.4.23.46 0.710
1zap A70Candidapepsin-2 3.4.23.24 0.706
2jji 0QSEndothiapepsin 3.4.23.22 0.706
2xfi XFIBeta-secretase 1 3.4.23.46 0.703
1bxo PP7Penicillopepsin-1 3.4.23.20 0.702
2b8l 5HABeta-secretase 1 3.4.23.46 0.701
4dpf 0LGBeta-secretase 1 3.4.23.46 0.701
2xfj VG5Beta-secretase 1 3.4.23.46 0.698
3prs RITEndothiapepsin 3.4.23.22 0.696
1e81 M91Endothiapepsin 3.4.23.22 0.695
3lpk Z76Beta-secretase 1 3.4.23.46 0.695
3dv5 BAVBeta-secretase 1 3.4.23.46 0.692
3lpi Z74Beta-secretase 1 3.4.23.46 0.692
2vnm CM8Beta-secretase 1 3.4.23.46 0.685
3veu 0GOBeta-secretase 1 3.4.23.46 0.685
2viz VG4Beta-secretase 1 3.4.23.46 0.684
2vnn CM7Beta-secretase 1 3.4.23.46 0.684
2wf1 ZY1Beta-secretase 1 3.4.23.46 0.683
2vie VG0Beta-secretase 1 3.4.23.46 0.682
3r2f PB0Beta-secretase 1 3.4.23.46 0.681
1xs7 MMIBeta-secretase 1 3.4.23.46 0.680
2wez ZYEBeta-secretase 1 3.4.23.46 0.679
2oah QINBeta-secretase 1 3.4.23.46 0.678
4k8s 1QTBeta-secretase 1 3.4.23.46 0.677
4ke1 1R6Beta-secretase 1 3.4.23.46 0.677
2wf0 ZY0Beta-secretase 1 3.4.23.46 0.676
2web PP4Penicillopepsin-1 3.4.23.20 0.674
2wf2 ZY2Beta-secretase 1 3.4.23.46 0.670
3k5c 0BIBeta-secretase 1 3.4.23.46 0.668
3own 3OWRenin 3.4.23.15 0.667
4dpi 0N1Beta-secretase 1 3.4.23.46 0.663
2wf3 ZY3Beta-secretase 1 3.4.23.46 0.661
2qzl IXSBeta-secretase 1 3.4.23.46 0.660
3ohf 3HFBeta-secretase 1 3.4.23.46 0.660
3cic 316Beta-secretase 1 3.4.23.46 0.655