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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
3a5z KAA Elongation factor P--(R)-beta-lysine ligase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3a5z KAAElongation factor P--(R)-beta-lysine ligase / 1.281
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 1.121
3e9h KAALysine--tRNA ligase 6.1.1.6 0.912
3e9i XAHLysine--tRNA ligase 6.1.1.6 0.852
1c0a AMOAspartate--tRNA ligase / 0.851
3vqv ANPPyrrolysine--tRNA ligase / 0.829
4xeo A5AAlanine--tRNA ligase, cytoplasmic / 0.814
4bwa N0BPyrrolysine--tRNA ligase / 0.779
3pzc GAPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.772
4bw9 ANPPyrrolysine--tRNA ligase / 0.762
1fyf SSAThreonine--tRNA ligase 6.1.1.3 0.752
3mey ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.748
1nj5 P5AProline--tRNA ligase / 0.737
1nj6 A5AProline--tRNA ligase / 0.737
3bju ATPLysine--tRNA ligase 6.1.1.6 0.733
3vqx BLKPyrrolysine--tRNA ligase / 0.693
3m4p 4ADAsparaginyl-tRNA synthetase, putative / 0.687
4h2u ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.685
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.676
2i4m PSDProline--tRNA ligase 6.1.1.15 0.676
2zt5 B4PGlycine--tRNA ligase / 0.674
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.674
2aly YSAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.668
2i4n 5CAProline--tRNA ligase 6.1.1.15 0.668
3ufg ATPGlycine--tRNA ligase alpha subunit / 0.665
4s1b 2BALmo1466 protein / 0.659
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.658
5ckw ANPUncharacterized protein / 0.656
2gl0 ADNUncharacterized protein / 0.655
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.655