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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
4h2u ATP Amino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4h2u ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 1.139
3pzc GAPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.909
3mey ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.881
4bw9 ANPPyrrolysine--tRNA ligase / 0.770
1fyf SSAThreonine--tRNA ligase 6.1.1.3 0.752
4h2w 5GPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.730
3vqv ANPPyrrolysine--tRNA ligase / 0.726
1nj6 A5AProline--tRNA ligase / 0.708
2q7h YLYPyrrolysine--tRNA ligase / 0.707
4xeo A5AAlanine--tRNA ligase, cytoplasmic / 0.705
3e9i XAHLysine--tRNA ligase 6.1.1.6 0.692
3a5z KAAElongation factor P--(R)-beta-lysine ligase / 0.685
4bwa N0BPyrrolysine--tRNA ligase / 0.681
3bju ATPLysine--tRNA ligase 6.1.1.6 0.674
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.671
3ufg ATPGlycine--tRNA ligase alpha subunit / 0.666
1b7y FYAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.651
3e9h KAALysine--tRNA ligase 6.1.1.6 0.651