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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
1c0a AMO Aspartate--tRNA ligase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1c0a AMOAspartate--tRNA ligase / 1.266
3a5z KAAElongation factor P--(R)-beta-lysine ligase / 0.851
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.828
3e9h KAALysine--tRNA ligase 6.1.1.6 0.825
3bju ATPLysine--tRNA ligase 6.1.1.6 0.798
4bwa N0BPyrrolysine--tRNA ligase / 0.782
1fyf SSAThreonine--tRNA ligase 6.1.1.3 0.780
3vqv ANPPyrrolysine--tRNA ligase / 0.773
4xeo A5AAlanine--tRNA ligase, cytoplasmic / 0.772
2q7h YLYPyrrolysine--tRNA ligase / 0.764
1nj5 P5AProline--tRNA ligase / 0.753
4bw9 ANPPyrrolysine--tRNA ligase / 0.731
1nj6 A5AProline--tRNA ligase / 0.729
3e9i XAHLysine--tRNA ligase 6.1.1.6 0.726
3m4p 4ADAsparaginyl-tRNA synthetase, putative / 0.721
3pzc GAPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.719
2i4m PSDProline--tRNA ligase 6.1.1.15 0.706
3mey ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.698
1b7y FYAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.688
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.671
3vqx BLKPyrrolysine--tRNA ligase / 0.671
2x86 ADPADP-L-glycero-D-manno-heptose-6-epimerase / 0.660
2aly YSAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.658
2gl0 ADNUncharacterized protein / 0.655
3fvu IACKynurenine--oxoglutarate transaminase 1 2.6.1.7 0.654
4w5k PLPAspartate aminotransferase, mitochondrial / 0.654
2o8b ADPDNA mismatch repair protein Msh2 / 0.651