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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
2vnm CM8 Beta-secretase 1 3.4.23.46

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2vnm CM8Beta-secretase 1 3.4.23.46 1.300
2vnn CM7Beta-secretase 1 3.4.23.46 1.239
2vj7 VG6Beta-secretase 1 3.4.23.46 1.228
2vj6 VG5Beta-secretase 1 3.4.23.46 1.163
2wf0 ZY0Beta-secretase 1 3.4.23.46 1.154
2viz VG4Beta-secretase 1 3.4.23.46 1.149
2xfj VG5Beta-secretase 1 3.4.23.46 1.148
2xfk AA9Beta-secretase 1 3.4.23.46 1.133
2wf2 ZY2Beta-secretase 1 3.4.23.46 1.126
2vie VG0Beta-secretase 1 3.4.23.46 1.120
2vij C44Beta-secretase 1 3.4.23.46 1.111
2wez ZYEBeta-secretase 1 3.4.23.46 1.103
2wf3 ZY3Beta-secretase 1 3.4.23.46 1.096
2vj9 VG7Beta-secretase 1 3.4.23.46 1.073
2xfi XFIBeta-secretase 1 3.4.23.46 1.066
2wf1 ZY1Beta-secretase 1 3.4.23.46 1.064
2viy VG3Beta-secretase 1 3.4.23.46 1.059
2wf4 ZY4Beta-secretase 1 3.4.23.46 1.037
4fco 0U4Beta-secretase 1 3.4.23.46 1.034
2b8l 5HABeta-secretase 1 3.4.23.46 1.012
4dpf 0LGBeta-secretase 1 3.4.23.46 1.002
2b8v 3BNBeta-secretase 1 3.4.23.46 0.993
2p8h MY9Beta-secretase 1 3.4.23.46 0.982
4k9h 1QUBeta-secretase 1 3.4.23.46 0.949
2iqg F2IBeta-secretase 1 3.4.23.46 0.947
3k5g BJCBeta-secretase 1 3.4.23.46 0.937
2qzl IXSBeta-secretase 1 3.4.23.46 0.934
4ewo 996Beta-secretase 1 3.4.23.46 0.931
3veu 0GOBeta-secretase 1 3.4.23.46 0.928
4dpi 0N1Beta-secretase 1 3.4.23.46 0.928
4exg 916Beta-secretase 1 3.4.23.46 0.926
3nsh 957Beta-secretase 1 3.4.23.46 0.922
4i0i 957Beta-secretase 1 3.4.23.46 0.922
3k5c 0BIBeta-secretase 1 3.4.23.46 0.917
2vkm BSDBeta-secretase 1 3.4.23.46 0.908
3i25 MV7Beta-secretase 1 3.4.23.46 0.895
3ohf 3HFBeta-secretase 1 3.4.23.46 0.893
3cib 314Beta-secretase 1 3.4.23.46 0.888
4i0h 1BLBeta-secretase 1 3.4.23.46 0.884
4dus 0MPBeta-secretase 1 3.4.23.46 0.881
4ke1 1R6Beta-secretase 1 3.4.23.46 0.874
3cid 318Beta-secretase 1 3.4.23.46 0.872
3qi1 C6ABeta-secretase 1 3.4.23.46 0.867
3ohh 3HHBeta-secretase 1 3.4.23.46 0.857
3dm6 757Beta-secretase 1 3.4.23.46 0.854
4gid 0GHBeta-secretase 1 3.4.23.46 0.848
3ixj 586Beta-secretase 1 3.4.23.46 0.840
3pi5 3P5Beta-secretase 1 3.4.23.46 0.840
4ke0 1R8Beta-secretase 1 3.4.23.46 0.839
2p83 MR0Beta-secretase 1 3.4.23.46 0.838
3lpk Z76Beta-secretase 1 3.4.23.46 0.838
3r2f PB0Beta-secretase 1 3.4.23.46 0.829
1w51 L01Beta-secretase 1 3.4.23.46 0.824
4k8s 1QTBeta-secretase 1 3.4.23.46 0.822
3dv5 BAVBeta-secretase 1 3.4.23.46 0.818
3lpj Z75Beta-secretase 1 3.4.23.46 0.806
2fdp FRPBeta-secretase 1 3.4.23.46 0.800
2oah QINBeta-secretase 1 3.4.23.46 0.798
3qbh QBHBeta-secretase 1 3.4.23.46 0.795
2hiz LIJBeta-secretase 1 3.4.23.46 0.787
3cic 316Beta-secretase 1 3.4.23.46 0.787
3dv1 AR9Beta-secretase 1 3.4.23.46 0.761
2p4j 23IBeta-secretase 1 3.4.23.46 0.756
3ixk 929Beta-secretase 1 3.4.23.46 0.755
3vg1 0GTBeta-secretase 1 3.4.23.46 0.741
3n4l 842Beta-secretase 1 3.4.23.46 0.736
3tpr 5HABeta-secretase 1 3.4.23.46 0.722
2g94 ZPQBeta-secretase 1 3.4.23.46 0.718
2hm1 LIQBeta-secretase 1 3.4.23.46 0.703
3k5d XLIBeta-secretase 1 3.4.23.46 0.703
4lxm 1YUBeta-secretase 1 3.4.23.46 0.703
2f3e AXQBeta-secretase 1 3.4.23.46 0.700
3duy AFJBeta-secretase 1 3.4.23.46 0.685
4lxa 1YSBeta-secretase 1 3.4.23.46 0.682
2ntr L00Beta-secretase 1 3.4.23.46 0.677
3lpi Z74Beta-secretase 1 3.4.23.46 0.675
3own 3OWRenin 3.4.23.15 0.675
3vf3 0GSBeta-secretase 1 3.4.23.46 0.665
2irz I02Beta-secretase 1 3.4.23.46 0.659
1qrp HH0Pepsin A-4 3.4.23.1 0.657
4d89 BXDBeta-secretase 1 3.4.23.46 0.656
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.655
1od1 0QSEndothiapepsin 3.4.23.22 0.652
1rne C60Renin 3.4.23.15 0.650