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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
2wf3 ZY3 Beta-secretase 1 3.4.23.46

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2wf3 ZY3Beta-secretase 1 3.4.23.46 1.167
2wf2 ZY2Beta-secretase 1 3.4.23.46 1.120
2wf1 ZY1Beta-secretase 1 3.4.23.46 1.098
2vnm CM8Beta-secretase 1 3.4.23.46 1.096
2wez ZYEBeta-secretase 1 3.4.23.46 1.081
2vnn CM7Beta-secretase 1 3.4.23.46 1.060
2vij C44Beta-secretase 1 3.4.23.46 1.057
2vj7 VG6Beta-secretase 1 3.4.23.46 1.050
2xfj VG5Beta-secretase 1 3.4.23.46 1.050
2wf0 ZY0Beta-secretase 1 3.4.23.46 1.048
2viz VG4Beta-secretase 1 3.4.23.46 1.040
2vj6 VG5Beta-secretase 1 3.4.23.46 1.035
2xfk AA9Beta-secretase 1 3.4.23.46 1.013
2b8l 5HABeta-secretase 1 3.4.23.46 1.011
2viy VG3Beta-secretase 1 3.4.23.46 1.005
2wf4 ZY4Beta-secretase 1 3.4.23.46 1.003
2xfi XFIBeta-secretase 1 3.4.23.46 1.000
2vie VG0Beta-secretase 1 3.4.23.46 0.999
2vj9 VG7Beta-secretase 1 3.4.23.46 0.992
4fco 0U4Beta-secretase 1 3.4.23.46 0.991
2p8h MY9Beta-secretase 1 3.4.23.46 0.980
2b8v 3BNBeta-secretase 1 3.4.23.46 0.943
4dpf 0LGBeta-secretase 1 3.4.23.46 0.922
4dpi 0N1Beta-secretase 1 3.4.23.46 0.879
2vkm BSDBeta-secretase 1 3.4.23.46 0.877
3veu 0GOBeta-secretase 1 3.4.23.46 0.877
3k5c 0BIBeta-secretase 1 3.4.23.46 0.874
4k9h 1QUBeta-secretase 1 3.4.23.46 0.873
4ewo 996Beta-secretase 1 3.4.23.46 0.872
3ohf 3HFBeta-secretase 1 3.4.23.46 0.859
4exg 916Beta-secretase 1 3.4.23.46 0.854
3nsh 957Beta-secretase 1 3.4.23.46 0.848
4i0i 957Beta-secretase 1 3.4.23.46 0.848
2qzl IXSBeta-secretase 1 3.4.23.46 0.843
3cid 318Beta-secretase 1 3.4.23.46 0.840
3i25 MV7Beta-secretase 1 3.4.23.46 0.840
4gid 0GHBeta-secretase 1 3.4.23.46 0.836
3ixj 586Beta-secretase 1 3.4.23.46 0.833
3dm6 757Beta-secretase 1 3.4.23.46 0.829
2iqg F2IBeta-secretase 1 3.4.23.46 0.823
3dv5 BAVBeta-secretase 1 3.4.23.46 0.817
3qi1 C6ABeta-secretase 1 3.4.23.46 0.817
4i0h 1BLBeta-secretase 1 3.4.23.46 0.813
3ohh 3HHBeta-secretase 1 3.4.23.46 0.807
3ixk 929Beta-secretase 1 3.4.23.46 0.801
1w51 L01Beta-secretase 1 3.4.23.46 0.800
2hiz LIJBeta-secretase 1 3.4.23.46 0.792
2oah QINBeta-secretase 1 3.4.23.46 0.787
3cic 316Beta-secretase 1 3.4.23.46 0.786
3k5f AYHBeta-secretase 1 3.4.23.46 0.782
3pww ROCEndothiapepsin 3.4.23.22 0.778
3cib 314Beta-secretase 1 3.4.23.46 0.775
3r2f PB0Beta-secretase 1 3.4.23.46 0.774
2fdp FRPBeta-secretase 1 3.4.23.46 0.764
2p83 MR0Beta-secretase 1 3.4.23.46 0.763
4ke1 1R6Beta-secretase 1 3.4.23.46 0.763
4ke0 1R8Beta-secretase 1 3.4.23.46 0.761
3lpj Z75Beta-secretase 1 3.4.23.46 0.747
3n4l 842Beta-secretase 1 3.4.23.46 0.737
1gvv 0GMEndothiapepsin 3.4.23.22 0.710
3pi5 3P5Beta-secretase 1 3.4.23.46 0.710
3qbh QBHBeta-secretase 1 3.4.23.46 0.703
2g94 ZPQBeta-secretase 1 3.4.23.46 0.696
3dv1 AR9Beta-secretase 1 3.4.23.46 0.695
4d89 BXDBeta-secretase 1 3.4.23.46 0.694
2f3e AXQBeta-secretase 1 3.4.23.46 0.692
4k8s 1QTBeta-secretase 1 3.4.23.46 0.684
2ntr L00Beta-secretase 1 3.4.23.46 0.675
3lpk Z76Beta-secretase 1 3.4.23.46 0.675
3lpi Z74Beta-secretase 1 3.4.23.46 0.674
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.673
3vg1 0GTBeta-secretase 1 3.4.23.46 0.673
2hm1 LIQBeta-secretase 1 3.4.23.46 0.668
2ph6 712Beta-secretase 1 3.4.23.46 0.668
3k5g BJCBeta-secretase 1 3.4.23.46 0.666
1gvt 2ZSEndothiapepsin 3.4.23.22 0.665
3dcr KVSProtease / 0.665
1b6m PI6Gag-Pol polyprotein 3.4.23.16 0.662
3duy AFJBeta-secretase 1 3.4.23.46 0.661
1b6p PI7Gag-Pol polyprotein 3.4.23.16 0.656
1e80 0GQEndothiapepsin 3.4.23.22 0.654
1ppm 0P1Penicillopepsin-1 3.4.23.20 0.654
4y38 0A9Endothiapepsin 3.4.23.22 0.651