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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
3vhi VHI Avidin

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3vhi VHIAvidin / 1.209
3vgw NVZAvidin / 0.954
4bcs BTNAvidin-related protein 4/5 / 0.892
1y52 BTNAvidin-related protein 4/5 / 0.860
2jgs BTNAvidin / 0.849
2fhl BNIAvidin-related protein 4/5 / 0.843
2fhn BNIAvidin-related protein 4/5 / 0.842
2c4i BTNAvidin / 0.840
2uyw BTNAvd protein / 0.823
3vhm NPKAvidin / 0.816
2izh BTNStreptavidin / 0.811
3ry2 BTNStreptavidin / 0.804
2y3f BTNStreptavidin / 0.801
1nqm BTNStreptavidin / 0.799
1swe BTNStreptavidin / 0.798
2izf BTNStreptavidin / 0.796
2rte BTNStreptavidin / 0.790
1mk5 BTNStreptavidin / 0.789
1lcw SHMStreptavidin / 0.776
1n9m BTNStreptavidin / 0.775
4z28 BTNHoefavidin / 0.774
4gda BTNStreptavidin / 0.770
2zsc BTNTamavidin2 / 0.767
2izg BTNStreptavidin / 0.766
2izi BTNStreptavidin / 0.765
3wyq BTNStreptavidin / 0.765
2izl IMIStreptavidin / 0.764
1i9h BNIStreptavidin / 0.762
3wyp BSOStreptavidin / 0.762
1luq BTNStreptavidin / 0.760
3wzn BTNStreptavidin / 0.758
1nc9 IMIStreptavidin / 0.757
2izj BTNStreptavidin / 0.757
4yvb BTNStreptavidin / 0.757
4bj8 BTNAvidin / 0.755
2rtg BTNStreptavidin / 0.752
1swn BTNStreptavidin / 0.751
1df8 BTNStreptavidin / 0.750
4gd9 BTNStreptavidin / 0.749
2rtd BTNStreptavidin / 0.747
1swr BTNStreptavidin / 0.746
2rtf BTNStreptavidin / 0.746
3rdo BTNStreptavidin / 0.746
1swt BTNStreptavidin / 0.738
4ggz BTNBll1558 protein / 0.738
3ew2 BTNHypothetical conserved protein / 0.734
1n43 BTNStreptavidin / 0.729
2rtn IMIStreptavidin / 0.729
2avi BTNAvidin / 0.726
2rto IMIStreptavidin / 0.726
4dne DTBStreptavidin / 0.725
1swp BTNStreptavidin / 0.724
1mep BTNStreptavidin / 0.720
1ndj BTNStreptavidin / 0.715
1stp BTNStreptavidin / 0.713
4bx7 B4FStreptavidin / 0.713
1lcz BH7Streptavidin / 0.710
2rtp IMIStreptavidin / 0.708
3t2w BTNAvidin/streptavidin / 0.700
3rdq DTBStreptavidin / 0.698
1swp BTQStreptavidin / 0.693
1swd BTNStreptavidin / 0.669
1lel BH7Avidin / 0.661
3akn 11DFatty acid-binding protein, intestinal / 0.654