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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
4gid 0GH Beta-secretase 1 3.4.23.46

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4gid 0GHBeta-secretase 1 3.4.23.46 1.437
2qzl IXSBeta-secretase 1 3.4.23.46 1.252
4fco 0U4Beta-secretase 1 3.4.23.46 1.087
2b8l 5HABeta-secretase 1 3.4.23.46 1.078
2vkm BSDBeta-secretase 1 3.4.23.46 1.055
3dm6 757Beta-secretase 1 3.4.23.46 1.032
3i25 MV7Beta-secretase 1 3.4.23.46 1.029
3ixj 586Beta-secretase 1 3.4.23.46 1.014
2p8h MY9Beta-secretase 1 3.4.23.46 0.970
2xfk AA9Beta-secretase 1 3.4.23.46 0.901
2b8v 3BNBeta-secretase 1 3.4.23.46 0.899
2xfi XFIBeta-secretase 1 3.4.23.46 0.899
4dpf 0LGBeta-secretase 1 3.4.23.46 0.888
2viz VG4Beta-secretase 1 3.4.23.46 0.886
2xfj VG5Beta-secretase 1 3.4.23.46 0.880
2vj6 VG5Beta-secretase 1 3.4.23.46 0.862
2vj7 VG6Beta-secretase 1 3.4.23.46 0.858
2wf1 ZY1Beta-secretase 1 3.4.23.46 0.854
2wez ZYEBeta-secretase 1 3.4.23.46 0.851
2vnm CM8Beta-secretase 1 3.4.23.46 0.848
2wf2 ZY2Beta-secretase 1 3.4.23.46 0.839
2wf3 ZY3Beta-secretase 1 3.4.23.46 0.836
2vnn CM7Beta-secretase 1 3.4.23.46 0.832
2is0 I03Beta-secretase 1 3.4.23.46 0.826
2vij C44Beta-secretase 1 3.4.23.46 0.821
2wf0 ZY0Beta-secretase 1 3.4.23.46 0.819
2irz I02Beta-secretase 1 3.4.23.46 0.815
2vj9 VG7Beta-secretase 1 3.4.23.46 0.809
2wf4 ZY4Beta-secretase 1 3.4.23.46 0.802
3ixk 929Beta-secretase 1 3.4.23.46 0.789
2p83 MR0Beta-secretase 1 3.4.23.46 0.779
3cid 318Beta-secretase 1 3.4.23.46 0.773
4k9h 1QUBeta-secretase 1 3.4.23.46 0.757
2oah QINBeta-secretase 1 3.4.23.46 0.754
2fdp FRPBeta-secretase 1 3.4.23.46 0.749
2ntr L00Beta-secretase 1 3.4.23.46 0.749
3ohf 3HFBeta-secretase 1 3.4.23.46 0.744
3cic 316Beta-secretase 1 3.4.23.46 0.742
2viy VG3Beta-secretase 1 3.4.23.46 0.738
3cib 314Beta-secretase 1 3.4.23.46 0.737
2f3e AXQBeta-secretase 1 3.4.23.46 0.728
2vie VG0Beta-secretase 1 3.4.23.46 0.722
3k5c 0BIBeta-secretase 1 3.4.23.46 0.718
3dv5 BAVBeta-secretase 1 3.4.23.46 0.715
2iqg F2IBeta-secretase 1 3.4.23.46 0.709
3k5f AYHBeta-secretase 1 3.4.23.46 0.704
2p4j 23IBeta-secretase 1 3.4.23.46 0.703
3own 3OWRenin 3.4.23.15 0.700
3r2f PB0Beta-secretase 1 3.4.23.46 0.698
3lpi Z74Beta-secretase 1 3.4.23.46 0.689
1w51 L01Beta-secretase 1 3.4.23.46 0.688
4dpi 0N1Beta-secretase 1 3.4.23.46 0.684
1bxq PP8Penicillopepsin-1 3.4.23.20 0.677
1xe5 5FEPlasmepsin-2 3.4.23.39 0.673
3nwq 2NCGag-Pol polyprotein 3.4.23.16 0.672
3lpk Z76Beta-secretase 1 3.4.23.46 0.671
2ph6 712Beta-secretase 1 3.4.23.46 0.670
3nsh 957Beta-secretase 1 3.4.23.46 0.669
4i0i 957Beta-secretase 1 3.4.23.46 0.669
1ppm 0P1Penicillopepsin-1 3.4.23.20 0.666
3dv1 AR9Beta-secretase 1 3.4.23.46 0.663
1bxo PP7Penicillopepsin-1 3.4.23.20 0.660
3lpj Z75Beta-secretase 1 3.4.23.46 0.660
1ppl 1Z7Penicillopepsin-1 3.4.23.20 0.659
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.658
3so9 017Pol protein / 0.658
3tpr 5HABeta-secretase 1 3.4.23.46 0.658