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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
3vgw NVZ Avidin

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3vgw NVZAvidin / 1.100
3vhi VHIAvidin / 0.954
1y52 BTNAvidin-related protein 4/5 / 0.921
4bcs BTNAvidin-related protein 4/5 / 0.904
2uyw BTNAvd protein / 0.903
2jgs BTNAvidin / 0.876
2c4i BTNAvidin / 0.874
2fhl BNIAvidin-related protein 4/5 / 0.870
2izh BTNStreptavidin / 0.827
1n9m BTNStreptavidin / 0.818
2uz2 BTNAvd protein / 0.811
2izf BTNStreptavidin / 0.807
3wyp BSOStreptavidin / 0.800
1n43 BTNStreptavidin / 0.799
1swe BTNStreptavidin / 0.798
3ry2 BTNStreptavidin / 0.792
2izg BTNStreptavidin / 0.791
2y3f BTNStreptavidin / 0.788
2rtd BTNStreptavidin / 0.787
1lcw SHMStreptavidin / 0.784
2rtf BTNStreptavidin / 0.783
2rte BTNStreptavidin / 0.782
4gda BTNStreptavidin / 0.778
1swn BTNStreptavidin / 0.776
3wyq BTNStreptavidin / 0.773
2rtg BTNStreptavidin / 0.769
4yvb BTNStreptavidin / 0.764
2izl IMIStreptavidin / 0.758
2izj BTNStreptavidin / 0.754
1mk5 BTNStreptavidin / 0.751
4bj8 BTNAvidin / 0.746
1swt BTNStreptavidin / 0.744
4dne DTBStreptavidin / 0.744
3rdo BTNStreptavidin / 0.743
4z28 BTNHoefavidin / 0.737
1stp BTNStreptavidin / 0.736
2rto IMIStreptavidin / 0.733
4bx7 B4FStreptavidin / 0.725
1df8 BTNStreptavidin / 0.718
1swp BTNStreptavidin / 0.717
1ndj BTNStreptavidin / 0.716
1luq BTNStreptavidin / 0.713
3wzn BTNStreptavidin / 0.706
2rtr IMIStreptavidin / 0.700
1lcz BH7Streptavidin / 0.699
4ggz BTNBll1558 protein / 0.699
2avi BTNAvidin / 0.695
1swr BTNStreptavidin / 0.688
2rtq IMIStreptavidin / 0.688
3rdq DTBStreptavidin / 0.683
4zea IMIEndothiapepsin 3.4.23.22 0.672
1mep BTNStreptavidin / 0.667
1swp BTQStreptavidin / 0.667
2rtp IMIStreptavidin / 0.665
2rtm IMIStreptavidin / 0.661
1nqm BTNStreptavidin / 0.653
4cav MYAGlycylpeptide N-tetradecanoyltransferase 2.3.1.97 0.652