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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
3e9h KAA Lysine--tRNA ligase 6.1.1.6

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3e9h KAALysine--tRNA ligase 6.1.1.6 1.333
3e9i XAHLysine--tRNA ligase 6.1.1.6 1.002
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.944
3a5z KAAElongation factor P--(R)-beta-lysine ligase / 0.912
1fyf SSAThreonine--tRNA ligase 6.1.1.3 0.841
4xeo A5AAlanine--tRNA ligase, cytoplasmic / 0.840
1c0a AMOAspartate--tRNA ligase / 0.825
4bw9 ANPPyrrolysine--tRNA ligase / 0.818
1nj5 P5AProline--tRNA ligase / 0.813
1nj6 A5AProline--tRNA ligase / 0.807
3bju ATPLysine--tRNA ligase 6.1.1.6 0.775
2q7h YLYPyrrolysine--tRNA ligase / 0.772
3vqv ANPPyrrolysine--tRNA ligase / 0.760
3mey ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.759
2aly YSAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.724
4bwa N0BPyrrolysine--tRNA ligase / 0.722
3pzc GAPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.708
2i4m PSDProline--tRNA ligase 6.1.1.15 0.686
2i4n 5CAProline--tRNA ligase 6.1.1.15 0.677
3m4p 4ADAsparaginyl-tRNA synthetase, putative / 0.669
1b7y FYAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.668
3ufg ATPGlycine--tRNA ligase alpha subunit / 0.667
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.658
3vqx BLKPyrrolysine--tRNA ligase / 0.655
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.655
1xmv ADPProtein RecA / 0.652
3ehj ACPSensor histidine kinase DesK 2.7.13.3 0.652
2zio AYBPyrrolysine--tRNA ligase / 0.651
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
4h2u ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.651