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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
3bju ATP Lysine--tRNA ligase 6.1.1.6

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3bju ATPLysine--tRNA ligase 6.1.1.6 1.285
4bw9 ANPPyrrolysine--tRNA ligase / 0.946
3vqv ANPPyrrolysine--tRNA ligase / 0.876
3mey ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.801
3e9i XAHLysine--tRNA ligase 6.1.1.6 0.800
1c0a AMOAspartate--tRNA ligase / 0.798
1fyf SSAThreonine--tRNA ligase 6.1.1.3 0.782
3e9h KAALysine--tRNA ligase 6.1.1.6 0.775
2q7h YLYPyrrolysine--tRNA ligase / 0.754
3pzc GAPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.742
3a5z KAAElongation factor P--(R)-beta-lysine ligase / 0.733
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.718
1nj6 A5AProline--tRNA ligase / 0.708
1nj5 P5AProline--tRNA ligase / 0.694
2zt7 ATPGlycine--tRNA ligase / 0.681
2idx ATPCob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial 2.5.1.17 0.675
4h2u ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.674
2aly YSAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.671
2zt5 B4PGlycine--tRNA ligase / 0.669
1eq2 ADQADP-L-glycero-D-manno-heptose-6-epimerase / 0.664
4au7 SAHHistone-lysine N-methyltransferase KMT5C 2.1.1.43 0.651