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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
2f3e AXQ Beta-secretase 1 3.4.23.46

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2f3e AXQBeta-secretase 1 3.4.23.46 1.460
2p4j 23IBeta-secretase 1 3.4.23.46 1.066
2g94 ZPQBeta-secretase 1 3.4.23.46 1.062
3duy AFJBeta-secretase 1 3.4.23.46 0.991
3k5d XLIBeta-secretase 1 3.4.23.46 0.981
3ixk 929Beta-secretase 1 3.4.23.46 0.927
3ixj 586Beta-secretase 1 3.4.23.46 0.920
3i25 MV7Beta-secretase 1 3.4.23.46 0.918
2f3f AXFBeta-secretase 1 3.4.23.46 0.915
3dv1 AR9Beta-secretase 1 3.4.23.46 0.905
3k5f AYHBeta-secretase 1 3.4.23.46 0.898
3dm6 757Beta-secretase 1 3.4.23.46 0.803
2qzl IXSBeta-secretase 1 3.4.23.46 0.778
2fdp FRPBeta-secretase 1 3.4.23.46 0.763
1od1 0QSEndothiapepsin 3.4.23.22 0.757
3dv5 BAVBeta-secretase 1 3.4.23.46 0.757
3k5c 0BIBeta-secretase 1 3.4.23.46 0.749
2p83 MR0Beta-secretase 1 3.4.23.46 0.740
2iqg F2IBeta-secretase 1 3.4.23.46 0.738
1eag A70Candidapepsin-2 3.4.23.24 0.733
3veu 0GOBeta-secretase 1 3.4.23.46 0.731
2wf0 ZY0Beta-secretase 1 3.4.23.46 0.730
2vnn CM7Beta-secretase 1 3.4.23.46 0.729
1bxq PP8Penicillopepsin-1 3.4.23.20 0.728
4gid 0GHBeta-secretase 1 3.4.23.46 0.728
2vie VG0Beta-secretase 1 3.4.23.46 0.727
1rne C60Renin 3.4.23.15 0.725
2hiz LIJBeta-secretase 1 3.4.23.46 0.723
3cic 316Beta-secretase 1 3.4.23.46 0.723
3own 3OXRenin 3.4.23.15 0.723
1gvv 0GMEndothiapepsin 3.4.23.22 0.720
1zap A70Candidapepsin-2 3.4.23.24 0.719
2web PP4Penicillopepsin-1 3.4.23.20 0.719
3cib 314Beta-secretase 1 3.4.23.46 0.717
3l5e BDWBeta-secretase 1 3.4.23.46 0.716
4dpf 0LGBeta-secretase 1 3.4.23.46 0.711
3cid 318Beta-secretase 1 3.4.23.46 0.709
2vj6 VG5Beta-secretase 1 3.4.23.46 0.708
3lpk Z76Beta-secretase 1 3.4.23.46 0.708
2wf1 ZY1Beta-secretase 1 3.4.23.46 0.706
2b8l 5HABeta-secretase 1 3.4.23.46 0.705
2wez ZYEBeta-secretase 1 3.4.23.46 0.703
3lpi Z74Beta-secretase 1 3.4.23.46 0.702
3nsh 957Beta-secretase 1 3.4.23.46 0.701
3own 3OWRenin 3.4.23.15 0.701
4i0i 957Beta-secretase 1 3.4.23.46 0.701
2vnm CM8Beta-secretase 1 3.4.23.46 0.700
3k5g BJCBeta-secretase 1 3.4.23.46 0.697
2oah QINBeta-secretase 1 3.4.23.46 0.693
2xfi XFIBeta-secretase 1 3.4.23.46 0.693
2viz VG4Beta-secretase 1 3.4.23.46 0.692
2wf2 ZY2Beta-secretase 1 3.4.23.46 0.692
2wf3 ZY3Beta-secretase 1 3.4.23.46 0.692
3pww ROCEndothiapepsin 3.4.23.22 0.689
2b8v 3BNBeta-secretase 1 3.4.23.46 0.688
1e80 0GQEndothiapepsin 3.4.23.22 0.686
1gvw 0EMEndothiapepsin 3.4.23.22 0.684
1w51 L01Beta-secretase 1 3.4.23.46 0.684
1w6h TITPlasmepsin-2 3.4.23.39 0.683
4dpi 0N1Beta-secretase 1 3.4.23.46 0.682
4k9h 1QUBeta-secretase 1 3.4.23.46 0.678
2vj7 VG6Beta-secretase 1 3.4.23.46 0.677
3qi1 C6ABeta-secretase 1 3.4.23.46 0.677
2vkm BSDBeta-secretase 1 3.4.23.46 0.676
3r2f PB0Beta-secretase 1 3.4.23.46 0.674
4ke0 1R8Beta-secretase 1 3.4.23.46 0.673
2xfk AA9Beta-secretase 1 3.4.23.46 0.672
2xfj VG5Beta-secretase 1 3.4.23.46 0.667
3lpj Z75Beta-secretase 1 3.4.23.46 0.666
3dcr KVSProtease / 0.664
1psa 0ZLPepsin A 3.4.23.1 0.661
2jji 0QSEndothiapepsin 3.4.23.22 0.658
2viy VG3Beta-secretase 1 3.4.23.46 0.652
3ohf 3HFBeta-secretase 1 3.4.23.46 0.652
3prs RITEndothiapepsin 3.4.23.22 0.651
3d91 REMRenin 3.4.23.15 0.650