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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
3r2f PB0 Beta-secretase 1 3.4.23.46

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3r2f PB0Beta-secretase 1 3.4.23.46 1.404
3cib 314Beta-secretase 1 3.4.23.46 0.965
3cid 318Beta-secretase 1 3.4.23.46 0.904
3ohh 3HHBeta-secretase 1 3.4.23.46 0.877
3lpk Z76Beta-secretase 1 3.4.23.46 0.876
3veu 0GOBeta-secretase 1 3.4.23.46 0.874
2p83 MR0Beta-secretase 1 3.4.23.46 0.870
3qi1 C6ABeta-secretase 1 3.4.23.46 0.861
2xfk AA9Beta-secretase 1 3.4.23.46 0.840
3k5c 0BIBeta-secretase 1 3.4.23.46 0.840
2wf1 ZY1Beta-secretase 1 3.4.23.46 0.831
3nsh 957Beta-secretase 1 3.4.23.46 0.830
4i0i 957Beta-secretase 1 3.4.23.46 0.830
2vnm CM8Beta-secretase 1 3.4.23.46 0.829
3cic 316Beta-secretase 1 3.4.23.46 0.827
2wf2 ZY2Beta-secretase 1 3.4.23.46 0.826
4ke0 1R8Beta-secretase 1 3.4.23.46 0.821
4exg 916Beta-secretase 1 3.4.23.46 0.818
2vj7 VG6Beta-secretase 1 3.4.23.46 0.815
4fco 0U4Beta-secretase 1 3.4.23.46 0.812
3ohf 3HFBeta-secretase 1 3.4.23.46 0.811
2wez ZYEBeta-secretase 1 3.4.23.46 0.809
4k8s 1QTBeta-secretase 1 3.4.23.46 0.808
2xfi XFIBeta-secretase 1 3.4.23.46 0.804
2wf0 ZY0Beta-secretase 1 3.4.23.46 0.803
2vij C44Beta-secretase 1 3.4.23.46 0.799
2p8h MY9Beta-secretase 1 3.4.23.46 0.798
2vnn CM7Beta-secretase 1 3.4.23.46 0.794
4dh6 0KNBeta-secretase 1 3.4.23.46 0.794
3k5g BJCBeta-secretase 1 3.4.23.46 0.791
2vj6 VG5Beta-secretase 1 3.4.23.46 0.789
3dv5 BAVBeta-secretase 1 3.4.23.46 0.789
3qbh QBHBeta-secretase 1 3.4.23.46 0.789
2b8l 5HABeta-secretase 1 3.4.23.46 0.787
2wf4 ZY4Beta-secretase 1 3.4.23.46 0.784
2xfj VG5Beta-secretase 1 3.4.23.46 0.784
3dm6 757Beta-secretase 1 3.4.23.46 0.777
4i0h 1BLBeta-secretase 1 3.4.23.46 0.777
4dpf 0LGBeta-secretase 1 3.4.23.46 0.775
2wf3 ZY3Beta-secretase 1 3.4.23.46 0.774
4ewo 996Beta-secretase 1 3.4.23.46 0.773
2vj9 VG7Beta-secretase 1 3.4.23.46 0.769
3vf3 0GSBeta-secretase 1 3.4.23.46 0.767
4k9h 1QUBeta-secretase 1 3.4.23.46 0.767
2viz VG4Beta-secretase 1 3.4.23.46 0.763
2b8v 3BNBeta-secretase 1 3.4.23.46 0.760
2fdp FRPBeta-secretase 1 3.4.23.46 0.760
3pi5 3P5Beta-secretase 1 3.4.23.46 0.759
4i0j 842Beta-secretase 1 3.4.23.46 0.759
2viy VG3Beta-secretase 1 3.4.23.46 0.752
3lpj Z75Beta-secretase 1 3.4.23.46 0.749
3skg PB8Beta-secretase 1 3.4.23.46 0.747
3vg1 0GTBeta-secretase 1 3.4.23.46 0.734
4lxm 1YUBeta-secretase 1 3.4.23.46 0.732
3dv1 AR9Beta-secretase 1 3.4.23.46 0.725
3ixj 586Beta-secretase 1 3.4.23.46 0.721
3lpi Z74Beta-secretase 1 3.4.23.46 0.721
3pww ROCEndothiapepsin 3.4.23.22 0.721
3n4l 842Beta-secretase 1 3.4.23.46 0.718
2iqg F2IBeta-secretase 1 3.4.23.46 0.715
2oah QINBeta-secretase 1 3.4.23.46 0.715
2hm1 LIQBeta-secretase 1 3.4.23.46 0.707
1od1 0QSEndothiapepsin 3.4.23.22 0.699
2f3f AXFBeta-secretase 1 3.4.23.46 0.699
3k5d XLIBeta-secretase 1 3.4.23.46 0.698
4gid 0GHBeta-secretase 1 3.4.23.46 0.698
2jjj 0QSEndothiapepsin 3.4.23.22 0.694
2hiz LIJBeta-secretase 1 3.4.23.46 0.692
2jji 0QSEndothiapepsin 3.4.23.22 0.692
3i25 MV7Beta-secretase 1 3.4.23.46 0.686
1bxo PP7Penicillopepsin-1 3.4.23.20 0.682
2g94 ZPQBeta-secretase 1 3.4.23.46 0.681
3duy AFJBeta-secretase 1 3.4.23.46 0.681
1e81 M91Endothiapepsin 3.4.23.22 0.679
3ixk 929Beta-secretase 1 3.4.23.46 0.677
1eag A70Candidapepsin-2 3.4.23.24 0.674
2f3e AXQBeta-secretase 1 3.4.23.46 0.674
2p4j 23IBeta-secretase 1 3.4.23.46 0.673
1ppm 0P1Penicillopepsin-1 3.4.23.20 0.672
1rne C60Renin 3.4.23.15 0.670
3tpr 5HABeta-secretase 1 3.4.23.46 0.666
2g20 L1ARenin 3.4.23.15 0.655
1bxq PP8Penicillopepsin-1 3.4.23.20 0.652
1e80 0GQEndothiapepsin 3.4.23.22 0.651