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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
1ppm 0P1 Penicillopepsin-1 3.4.23.20

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1ppm 0P1Penicillopepsin-1 3.4.23.20 1.303
1ppl 1Z7Penicillopepsin-1 3.4.23.20 1.075
1bxq PP8Penicillopepsin-1 3.4.23.20 1.042
1ppk IVVPenicillopepsin-1 3.4.23.20 1.002
1bxo PP7Penicillopepsin-1 3.4.23.20 0.987
2web PP4Penicillopepsin-1 3.4.23.20 0.916
1gvw 0EMEndothiapepsin 3.4.23.22 0.868
1od1 0QSEndothiapepsin 3.4.23.22 0.833
1gvt 2ZSEndothiapepsin 3.4.23.22 0.832
2jjj 0QSEndothiapepsin 3.4.23.22 0.827
1qrp HH0Pepsin A-4 3.4.23.1 0.786
2wed PP6Penicillopepsin-1 3.4.23.20 0.759
3dv1 AR9Beta-secretase 1 3.4.23.46 0.754
2wec PP5Penicillopepsin-1 3.4.23.20 0.748
3k5d XLIBeta-secretase 1 3.4.23.46 0.745
3duy AFJBeta-secretase 1 3.4.23.46 0.739
1psa 0ZLPepsin A 3.4.23.1 0.736
1e81 M91Endothiapepsin 3.4.23.22 0.733
2jji 0QSEndothiapepsin 3.4.23.22 0.732
1rne C60Renin 3.4.23.15 0.731
3prs RITEndothiapepsin 3.4.23.22 0.729
2p4j 23IBeta-secretase 1 3.4.23.46 0.726
1e82 M90Endothiapepsin 3.4.23.22 0.724
2g94 ZPQBeta-secretase 1 3.4.23.46 0.723
2wea PP6Penicillopepsin-1 3.4.23.20 0.719
2g20 L1ARenin 3.4.23.15 0.674
3r2f PB0Beta-secretase 1 3.4.23.46 0.672
4gid 0GHBeta-secretase 1 3.4.23.46 0.666
4ewo 996Beta-secretase 1 3.4.23.46 0.661
1xe5 5FEPlasmepsin-2 3.4.23.39 0.660
1eag A70Candidapepsin-2 3.4.23.24 0.659
2vij C44Beta-secretase 1 3.4.23.46 0.656
3d91 REMRenin 3.4.23.15 0.655
1w51 L01Beta-secretase 1 3.4.23.46 0.654
2wf3 ZY3Beta-secretase 1 3.4.23.46 0.654
3tne RITCandidapepsin-1 3.4.23.24 0.654