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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
4nbj D3Y D-tyrosyl-tRNA(Tyr) deacylase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4nbj D3YD-tyrosyl-tRNA(Tyr) deacylase / 0.943
4nbi D3YD-tyrosyl-tRNA(Tyr) deacylase / 0.863
4rrg A3TThreonine--tRNA ligase 6.1.1.3 0.740
4rrj A3SProbable threonine--tRNA ligase 2 6.1.1.3 0.717
3pd4 A3GThreonine--tRNA ligase 6.1.1.3 0.699
4rr9 A3SProbable threonine--tRNA ligase 2 6.1.1.3 0.697
4rr7 A3SProbable threonine--tRNA ligase 2 6.1.1.3 0.694
4rrl A3SProbable threonine--tRNA ligase 2 6.1.1.3 0.692
4rrm A3TProbable threonine--tRNA ligase 2 6.1.1.3 0.692
3pd3 A3TThreonine--tRNA ligase 6.1.1.3 0.691
4rr6 A3SProbable threonine--tRNA ligase 2 6.1.1.3 0.691
4rri A3TProbable threonine--tRNA ligase 2 6.1.1.3 0.691
4rr8 A3SProbable threonine--tRNA ligase 2 6.1.1.3 0.689
4rrh A3SProbable threonine--tRNA ligase 2 6.1.1.3 0.688
2hl2 SSAThreonine--tRNA ligase 6.1.1.3 0.681
3pd2 A3SThreonine--tRNA ligase 6.1.1.3 0.681
4rrk A3TProbable threonine--tRNA ligase 2 6.1.1.3 0.680
4rrb A3TProbable threonine--tRNA ligase 2 6.1.1.3 0.678
4rrd A3TProbable threonine--tRNA ligase 2 6.1.1.3 0.671
4rra A3TProbable threonine--tRNA ligase 2 6.1.1.3 0.667
4rrq A3SThreonine--tRNA ligase 6.1.1.3 0.662
2hl0 A3SThreonine--tRNA ligase 6.1.1.3 0.660
2hl1 A3SThreonine--tRNA ligase 6.1.1.3 0.656
4s34 ANPMitogen-activated protein kinase 1 2.7.11.24 0.653
4rrc A3TProbable threonine--tRNA ligase 2 6.1.1.3 0.651