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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
3k5g BJC Beta-secretase 1 3.4.23.46

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3k5g BJCBeta-secretase 1 3.4.23.46 1.335
3veu 0GOBeta-secretase 1 3.4.23.46 1.025
2wf0 ZY0Beta-secretase 1 3.4.23.46 0.974
3dv5 BAVBeta-secretase 1 3.4.23.46 0.967
2vnn CM7Beta-secretase 1 3.4.23.46 0.955
2vj7 VG6Beta-secretase 1 3.4.23.46 0.937
2vnm CM8Beta-secretase 1 3.4.23.46 0.937
4k9h 1QUBeta-secretase 1 3.4.23.46 0.923
4dpi 0N1Beta-secretase 1 3.4.23.46 0.922
2wf1 ZY1Beta-secretase 1 3.4.23.46 0.920
3k5c 0BIBeta-secretase 1 3.4.23.46 0.918
4dpf 0LGBeta-secretase 1 3.4.23.46 0.913
2iqg F2IBeta-secretase 1 3.4.23.46 0.909
2hiz LIJBeta-secretase 1 3.4.23.46 0.905
2hm1 LIQBeta-secretase 1 3.4.23.46 0.902
2wf2 ZY2Beta-secretase 1 3.4.23.46 0.901
4fco 0U4Beta-secretase 1 3.4.23.46 0.900
4dus 0MPBeta-secretase 1 3.4.23.46 0.894
3ohf 3HFBeta-secretase 1 3.4.23.46 0.892
2viz VG4Beta-secretase 1 3.4.23.46 0.891
3vg1 0GTBeta-secretase 1 3.4.23.46 0.890
2vj6 VG5Beta-secretase 1 3.4.23.46 0.886
2b8v 3BNBeta-secretase 1 3.4.23.46 0.882
4lxk 1YTBeta-secretase 1 3.4.23.46 0.876
2xfk AA9Beta-secretase 1 3.4.23.46 0.875
3nsh 957Beta-secretase 1 3.4.23.46 0.875
4i0i 957Beta-secretase 1 3.4.23.46 0.875
2wez ZYEBeta-secretase 1 3.4.23.46 0.874
4lxa 1YSBeta-secretase 1 3.4.23.46 0.874
3cib 314Beta-secretase 1 3.4.23.46 0.873
2wf4 ZY4Beta-secretase 1 3.4.23.46 0.872
2xfi XFIBeta-secretase 1 3.4.23.46 0.872
2xfj VG5Beta-secretase 1 3.4.23.46 0.871
3lpj Z75Beta-secretase 1 3.4.23.46 0.871
2p8h MY9Beta-secretase 1 3.4.23.46 0.860
2p83 MR0Beta-secretase 1 3.4.23.46 0.855
2viy VG3Beta-secretase 1 3.4.23.46 0.852
2vkm BSDBeta-secretase 1 3.4.23.46 0.850
2vj9 VG7Beta-secretase 1 3.4.23.46 0.849
3cic 316Beta-secretase 1 3.4.23.46 0.840
3qbh QBHBeta-secretase 1 3.4.23.46 0.838
4lxm 1YUBeta-secretase 1 3.4.23.46 0.832
2fdp FRPBeta-secretase 1 3.4.23.46 0.827
3lpk Z76Beta-secretase 1 3.4.23.46 0.819
3cid 318Beta-secretase 1 3.4.23.46 0.817
2b8l 5HABeta-secretase 1 3.4.23.46 0.815
1w51 L01Beta-secretase 1 3.4.23.46 0.813
3r2f PB0Beta-secretase 1 3.4.23.46 0.791
3lpi Z74Beta-secretase 1 3.4.23.46 0.784
3dm6 757Beta-secretase 1 3.4.23.46 0.780
3vf3 0GSBeta-secretase 1 3.4.23.46 0.771
4i0j 842Beta-secretase 1 3.4.23.46 0.766
3pi5 3P5Beta-secretase 1 3.4.23.46 0.747
3k5f AYHBeta-secretase 1 3.4.23.46 0.744
3duy AFJBeta-secretase 1 3.4.23.46 0.742
3i25 MV7Beta-secretase 1 3.4.23.46 0.739
1gvv 0GMEndothiapepsin 3.4.23.22 0.737
2jjj 0QSEndothiapepsin 3.4.23.22 0.735
2web PP4Penicillopepsin-1 3.4.23.20 0.727
1od1 0QSEndothiapepsin 3.4.23.22 0.724
3ixj 586Beta-secretase 1 3.4.23.46 0.722
4k8s 1QTBeta-secretase 1 3.4.23.46 0.722
3own 3OXRenin 3.4.23.15 0.720
2jji 0QSEndothiapepsin 3.4.23.22 0.717
3tpr 5HABeta-secretase 1 3.4.23.46 0.711
1rne C60Renin 3.4.23.15 0.700
1bxo PP7Penicillopepsin-1 3.4.23.20 0.699
1ppl 1Z7Penicillopepsin-1 3.4.23.20 0.699
2qzl IXSBeta-secretase 1 3.4.23.46 0.699
2f3e AXQBeta-secretase 1 3.4.23.46 0.697
2g94 ZPQBeta-secretase 1 3.4.23.46 0.695
1bxq PP8Penicillopepsin-1 3.4.23.20 0.689
1e81 M91Endothiapepsin 3.4.23.22 0.688
1eag A70Candidapepsin-2 3.4.23.24 0.688
2p4j 23IBeta-secretase 1 3.4.23.46 0.688
1e82 M90Endothiapepsin 3.4.23.22 0.687
3k5d XLIBeta-secretase 1 3.4.23.46 0.686
1xe5 5FEPlasmepsin-2 3.4.23.39 0.685
1e80 0GQEndothiapepsin 3.4.23.22 0.683
4ke1 1R6Beta-secretase 1 3.4.23.46 0.683
1w6h TITPlasmepsin-2 3.4.23.39 0.678
3ixk 929Beta-secretase 1 3.4.23.46 0.671
2wf3 ZY3Beta-secretase 1 3.4.23.46 0.666
2vij C44Beta-secretase 1 3.4.23.46 0.664
2f3f AXFBeta-secretase 1 3.4.23.46 0.663
1gvw 0EMEndothiapepsin 3.4.23.22 0.661
3ohh 3HHBeta-secretase 1 3.4.23.46 0.659
1xe6 5FPPlasmepsin-2 3.4.23.39 0.658