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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
1fyf SSA Threonine--tRNA ligase 6.1.1.3

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1fyf SSAThreonine--tRNA ligase 6.1.1.3 1.313
1nj6 A5AProline--tRNA ligase / 0.845
3e9h KAALysine--tRNA ligase 6.1.1.6 0.841
1nj5 P5AProline--tRNA ligase / 0.828
4bw9 ANPPyrrolysine--tRNA ligase / 0.823
4xeo A5AAlanine--tRNA ligase, cytoplasmic / 0.820
2q7h YLYPyrrolysine--tRNA ligase / 0.786
3bju ATPLysine--tRNA ligase 6.1.1.6 0.782
1c0a AMOAspartate--tRNA ligase / 0.780
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.777
2aly YSAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.774
3e9i XAHLysine--tRNA ligase 6.1.1.6 0.769
3mey ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.768
3vqv ANPPyrrolysine--tRNA ligase / 0.758
3a5z KAAElongation factor P--(R)-beta-lysine ligase / 0.752
4h2u ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.752
1b7y FYAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.729
4bwa N0BPyrrolysine--tRNA ligase / 0.722
2i4m PSDProline--tRNA ligase 6.1.1.15 0.715
3pzc GAPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.684
3ufg ATPGlycine--tRNA ligase alpha subunit / 0.683
2zio AYBPyrrolysine--tRNA ligase / 0.681
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.672
1ses AHXSerine--tRNA ligase 6.1.1.11 0.671
2zt5 B4PGlycine--tRNA ligase / 0.662
2gl0 ADNUncharacterized protein / 0.660
4prx ADPDNA gyrase subunit B / 0.650