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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
3dv1 AR9 Beta-secretase 1 3.4.23.46

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3dv1 AR9Beta-secretase 1 3.4.23.46 1.378
3k5d XLIBeta-secretase 1 3.4.23.46 1.127
3duy AFJBeta-secretase 1 3.4.23.46 1.057
3k5f AYHBeta-secretase 1 3.4.23.46 1.026
2g94 ZPQBeta-secretase 1 3.4.23.46 0.993
2f3f AXFBeta-secretase 1 3.4.23.46 0.957
2p4j 23IBeta-secretase 1 3.4.23.46 0.957
2f3e AXQBeta-secretase 1 3.4.23.46 0.905
3i25 MV7Beta-secretase 1 3.4.23.46 0.839
3ixk 929Beta-secretase 1 3.4.23.46 0.812
2fdp FRPBeta-secretase 1 3.4.23.46 0.806
2hiz LIJBeta-secretase 1 3.4.23.46 0.805
2vj6 VG5Beta-secretase 1 3.4.23.46 0.775
2xfj VG5Beta-secretase 1 3.4.23.46 0.775
2viz VG4Beta-secretase 1 3.4.23.46 0.774
3dv5 BAVBeta-secretase 1 3.4.23.46 0.771
1rne C60Renin 3.4.23.15 0.764
2vnm CM8Beta-secretase 1 3.4.23.46 0.761
2xfk AA9Beta-secretase 1 3.4.23.46 0.756
2qzl IXSBeta-secretase 1 3.4.23.46 0.755
1ppm 0P1Penicillopepsin-1 3.4.23.20 0.754
2vnn CM7Beta-secretase 1 3.4.23.46 0.754
3dm6 757Beta-secretase 1 3.4.23.46 0.754
2hm1 LIQBeta-secretase 1 3.4.23.46 0.753
1gvw 0EMEndothiapepsin 3.4.23.22 0.750
3cid 318Beta-secretase 1 3.4.23.46 0.748
2iqg F2IBeta-secretase 1 3.4.23.46 0.745
1eag A70Candidapepsin-2 3.4.23.24 0.741
1gvt 2ZSEndothiapepsin 3.4.23.22 0.734
3veu 0GOBeta-secretase 1 3.4.23.46 0.733
2xfi XFIBeta-secretase 1 3.4.23.46 0.731
1bxq PP8Penicillopepsin-1 3.4.23.20 0.729
2wf0 ZY0Beta-secretase 1 3.4.23.46 0.729
2wez ZYEBeta-secretase 1 3.4.23.46 0.726
2wf1 ZY1Beta-secretase 1 3.4.23.46 0.726
3r2f PB0Beta-secretase 1 3.4.23.46 0.725
2jjj 0QSEndothiapepsin 3.4.23.22 0.724
2vie VG0Beta-secretase 1 3.4.23.46 0.723
3k5c 0BIBeta-secretase 1 3.4.23.46 0.721
1qrp HH0Pepsin A-4 3.4.23.1 0.718
1gvv 0GMEndothiapepsin 3.4.23.22 0.717
4dpi 0N1Beta-secretase 1 3.4.23.46 0.717
1bxo PP7Penicillopepsin-1 3.4.23.20 0.716
3cic 316Beta-secretase 1 3.4.23.46 0.715
4dpf 0LGBeta-secretase 1 3.4.23.46 0.710
2vj7 VG6Beta-secretase 1 3.4.23.46 0.706
4k9h 1QUBeta-secretase 1 3.4.23.46 0.698
2web PP4Penicillopepsin-1 3.4.23.20 0.697
1zap A70Candidapepsin-2 3.4.23.24 0.696
2wf3 ZY3Beta-secretase 1 3.4.23.46 0.695
2wf2 ZY2Beta-secretase 1 3.4.23.46 0.694
1e80 0GQEndothiapepsin 3.4.23.22 0.691
2vij C44Beta-secretase 1 3.4.23.46 0.691
1ppk IVVPenicillopepsin-1 3.4.23.20 0.689
2b8v 3BNBeta-secretase 1 3.4.23.46 0.688
2wf4 ZY4Beta-secretase 1 3.4.23.46 0.687
1bil 0IURenin 3.4.23.15 0.686
3cib 314Beta-secretase 1 3.4.23.46 0.682
1w6h TITPlasmepsin-2 3.4.23.39 0.678
4lxa 1YSBeta-secretase 1 3.4.23.46 0.678
3lpj Z75Beta-secretase 1 3.4.23.46 0.675
4k8s 1QTBeta-secretase 1 3.4.23.46 0.675
1xs7 MMIBeta-secretase 1 3.4.23.46 0.670
3lpi Z74Beta-secretase 1 3.4.23.46 0.665
4gid 0GHBeta-secretase 1 3.4.23.46 0.663
4lxm 1YUBeta-secretase 1 3.4.23.46 0.662
2oah QINBeta-secretase 1 3.4.23.46 0.659
3pi5 3P5Beta-secretase 1 3.4.23.46 0.659
3ohf 3HFBeta-secretase 1 3.4.23.46 0.656
3pww ROCEndothiapepsin 3.4.23.22 0.653
1e82 M90Endothiapepsin 3.4.23.22 0.652