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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
1nj5 P5A Proline--tRNA ligase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1nj5 P5AProline--tRNA ligase / 1.181
1nj6 A5AProline--tRNA ligase / 1.099
1fyf SSAThreonine--tRNA ligase 6.1.1.3 0.828
3e9h KAALysine--tRNA ligase 6.1.1.6 0.813
4xeo A5AAlanine--tRNA ligase, cytoplasmic / 0.763
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.758
1c0a AMOAspartate--tRNA ligase / 0.753
4bw9 ANPPyrrolysine--tRNA ligase / 0.740
3a5z KAAElongation factor P--(R)-beta-lysine ligase / 0.737
2i4n 5CAProline--tRNA ligase 6.1.1.15 0.734
2q7h YLYPyrrolysine--tRNA ligase / 0.732
2i4m PSDProline--tRNA ligase 6.1.1.15 0.730
3pzc GAPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.727
3e9i XAHLysine--tRNA ligase 6.1.1.6 0.711
3mey ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.701
3bju ATPLysine--tRNA ligase 6.1.1.6 0.694
3vqv ANPPyrrolysine--tRNA ligase / 0.675
2aly YSAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.671
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.665
4bwa N0BPyrrolysine--tRNA ligase / 0.664
1s16 ANPDNA topoisomerase 4 subunit B / 0.651
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.650