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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
3ixj 586 Beta-secretase 1 3.4.23.46

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3ixj 586Beta-secretase 1 3.4.23.46 1.690
3i25 MV7Beta-secretase 1 3.4.23.46 1.474
3ixk 929Beta-secretase 1 3.4.23.46 1.206
3dm6 757Beta-secretase 1 3.4.23.46 1.118
4fco 0U4Beta-secretase 1 3.4.23.46 1.065
2p4j 23IBeta-secretase 1 3.4.23.46 1.064
2b8l 5HABeta-secretase 1 3.4.23.46 1.043
4gid 0GHBeta-secretase 1 3.4.23.46 1.014
2p8h MY9Beta-secretase 1 3.4.23.46 0.971
2f3e AXQBeta-secretase 1 3.4.23.46 0.920
2xfk AA9Beta-secretase 1 3.4.23.46 0.918
2vkm BSDBeta-secretase 1 3.4.23.46 0.906
2b8v 3BNBeta-secretase 1 3.4.23.46 0.905
2wf4 ZY4Beta-secretase 1 3.4.23.46 0.884
2xfj VG5Beta-secretase 1 3.4.23.46 0.874
2viz VG4Beta-secretase 1 3.4.23.46 0.849
3cid 318Beta-secretase 1 3.4.23.46 0.849
2wf2 ZY2Beta-secretase 1 3.4.23.46 0.842
2vnm CM8Beta-secretase 1 3.4.23.46 0.840
2vj6 VG5Beta-secretase 1 3.4.23.46 0.838
2wf3 ZY3Beta-secretase 1 3.4.23.46 0.833
2f3f AXFBeta-secretase 1 3.4.23.46 0.830
2iqg F2IBeta-secretase 1 3.4.23.46 0.828
3k5f AYHBeta-secretase 1 3.4.23.46 0.828
2wf1 ZY1Beta-secretase 1 3.4.23.46 0.827
2oah QINBeta-secretase 1 3.4.23.46 0.825
2viy VG3Beta-secretase 1 3.4.23.46 0.823
2vj9 VG7Beta-secretase 1 3.4.23.46 0.823
4dpf 0LGBeta-secretase 1 3.4.23.46 0.821
2vij C44Beta-secretase 1 3.4.23.46 0.818
2vie VG0Beta-secretase 1 3.4.23.46 0.814
2qzl IXSBeta-secretase 1 3.4.23.46 0.809
2vj7 VG6Beta-secretase 1 3.4.23.46 0.809
3cib 314Beta-secretase 1 3.4.23.46 0.808
3duy AFJBeta-secretase 1 3.4.23.46 0.806
3cic 316Beta-secretase 1 3.4.23.46 0.798
3tpr 5HABeta-secretase 1 3.4.23.46 0.796
3k5c 0BIBeta-secretase 1 3.4.23.46 0.795
3lpi Z74Beta-secretase 1 3.4.23.46 0.765
2fdp FRPBeta-secretase 1 3.4.23.46 0.753
3own 3OWRenin 3.4.23.15 0.747
3qi1 C6ABeta-secretase 1 3.4.23.46 0.739
3lpj Z75Beta-secretase 1 3.4.23.46 0.738
2p83 MR0Beta-secretase 1 3.4.23.46 0.735
3k5g BJCBeta-secretase 1 3.4.23.46 0.722
1eag A70Candidapepsin-2 3.4.23.24 0.721
3r2f PB0Beta-secretase 1 3.4.23.46 0.721
1gvv 0GMEndothiapepsin 3.4.23.22 0.710
3lpk Z76Beta-secretase 1 3.4.23.46 0.709
4ke1 1R6Beta-secretase 1 3.4.23.46 0.708
1psa 0ZLPepsin A 3.4.23.1 0.707
1w51 L01Beta-secretase 1 3.4.23.46 0.707
1w6h TITPlasmepsin-2 3.4.23.39 0.699
4k8s 1QTBeta-secretase 1 3.4.23.46 0.697
3ohf 3HFBeta-secretase 1 3.4.23.46 0.695
3ohh 3HHBeta-secretase 1 3.4.23.46 0.694
1bil 0IURenin 3.4.23.15 0.691
1qrp HH0Pepsin A-4 3.4.23.1 0.687
2hb3 GRLProtease / 0.684
4j55 031Gag-Pol polyprotein 3.4.23.16 0.683
3o9a K14Pol polyprotein / 0.681
3o9f K2DGag-Pol polyprotein / 0.680
3k5d XLIBeta-secretase 1 3.4.23.46 0.676
2irz I02Beta-secretase 1 3.4.23.46 0.671
2qd7 065Gag-Pol polyprotein 3.4.23.16 0.670
2wf0 ZY0Beta-secretase 1 3.4.23.46 0.670
3i6o GR6Gag-Pol polyprotein 3.4.23.16 0.669
4k9h 1QUBeta-secretase 1 3.4.23.46 0.669
2i4x KGQProtease / 0.666
3o9g F53Gag-Pol polyprotein / 0.666
1bxo PP7Penicillopepsin-1 3.4.23.20 0.664
1t3r 017Gag-Pol polyprotein 3.4.23.16 0.664
2wez ZYEBeta-secretase 1 3.4.23.46 0.664
3o9d K19Pol polyprotein / 0.664
4a51 DQ8Kinesin-like protein KIF11 / 0.663
4dqh 017Gag-Pol polyprotein / 0.663
3sab F78Protease / 0.662
2hm1 LIQBeta-secretase 1 3.4.23.46 0.659
2vnn CM7Beta-secretase 1 3.4.23.46 0.659
2web PP4Penicillopepsin-1 3.4.23.20 0.659
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.657
1t7i 017Gag-Pol polyprotein 3.4.23.16 0.657
2ieo 017Protease / 0.657
2qi4 MZ6Gag-Pol polyprotein / 0.656
2qi6 MZ8Gag-Pol polyprotein / 0.656
4dqe 017Gag-Pol polyprotein / 0.654
2i0a MUIProtease / 0.653
3o99 K13Pol polyprotein / 0.653
3ucb 017Gag-Pol polyprotein / 0.653
2g94 ZPQBeta-secretase 1 3.4.23.46 0.651
2idw 017Protease / 0.651
2qci 065Gag-Pol polyprotein 3.4.23.16 0.651
3oxw 017Gag-Pol polyprotein 3.4.23.16 0.651
3s56 ROCProtease / 0.651
3o9b K2APol polyprotein / 0.650
3veu 0GOBeta-secretase 1 3.4.23.46 0.650