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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
3e9i XAH Lysine--tRNA ligase 6.1.1.6

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3e9i XAHLysine--tRNA ligase 6.1.1.6 1.347
3e9h KAALysine--tRNA ligase 6.1.1.6 1.002
3a5z KAAElongation factor P--(R)-beta-lysine ligase / 0.852
3bju ATPLysine--tRNA ligase 6.1.1.6 0.800
3vqv ANPPyrrolysine--tRNA ligase / 0.778
1fyf SSAThreonine--tRNA ligase 6.1.1.3 0.769
4bw9 ANPPyrrolysine--tRNA ligase / 0.765
3mey ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.760
4xeo A5AAlanine--tRNA ligase, cytoplasmic / 0.746
1nj6 A5AProline--tRNA ligase / 0.736
1c0a AMOAspartate--tRNA ligase / 0.726
3pzc GAPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.717
3ufg ATPGlycine--tRNA ligase alpha subunit / 0.712
1nj5 P5AProline--tRNA ligase / 0.711
4h2u ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.692
3m4p 4ADAsparaginyl-tRNA synthetase, putative / 0.677
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.662
2qen ADPWalker-Type ATPase / 0.661
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.658
2p0a ANPSynapsin-3 / 0.658
2zio AYBPyrrolysine--tRNA ligase / 0.657
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.655
4ffl ADPUncharacterized protein / 0.653
4ffr ATPUncharacterized protein / 0.650