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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
1ppl 1Z7 Penicillopepsin-1 3.4.23.20

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1ppl 1Z7Penicillopepsin-1 3.4.23.20 1.281
1ppk IVVPenicillopepsin-1 3.4.23.20 1.131
1bxq PP8Penicillopepsin-1 3.4.23.20 1.114
1ppm 0P1Penicillopepsin-1 3.4.23.20 1.075
1bxo PP7Penicillopepsin-1 3.4.23.20 1.069
2web PP4Penicillopepsin-1 3.4.23.20 0.903
1od1 0QSEndothiapepsin 3.4.23.22 0.877
2jjj 0QSEndothiapepsin 3.4.23.22 0.865
1gvw 0EMEndothiapepsin 3.4.23.22 0.856
1gvt 2ZSEndothiapepsin 3.4.23.22 0.809
2jji 0QSEndothiapepsin 3.4.23.22 0.798
2wed PP6Penicillopepsin-1 3.4.23.20 0.795
1qrp HH0Pepsin A-4 3.4.23.1 0.794
2wec PP5Penicillopepsin-1 3.4.23.20 0.765
1e82 M90Endothiapepsin 3.4.23.22 0.763
1e81 M91Endothiapepsin 3.4.23.22 0.762
3prs RITEndothiapepsin 3.4.23.22 0.754
1gvv 0GMEndothiapepsin 3.4.23.22 0.752
2wea PP6Penicillopepsin-1 3.4.23.20 0.748
1psa 0ZLPepsin A 3.4.23.1 0.738
3duy AFJBeta-secretase 1 3.4.23.46 0.736
2p4j 23IBeta-secretase 1 3.4.23.46 0.700
3k5g BJCBeta-secretase 1 3.4.23.46 0.699
3i25 MV7Beta-secretase 1 3.4.23.46 0.695
1e80 0GQEndothiapepsin 3.4.23.22 0.690
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.685
1bil 0IURenin 3.4.23.15 0.681
3tne RITCandidapepsin-1 3.4.23.24 0.664
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.662
2g20 L1ARenin 3.4.23.15 0.662
1eag A70Candidapepsin-2 3.4.23.24 0.659
1zap A70Candidapepsin-2 3.4.23.24 0.659
4gid 0GHBeta-secretase 1 3.4.23.46 0.659
2b8l 5HABeta-secretase 1 3.4.23.46 0.655
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.654