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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
3pzc GAP 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
3pzc GAPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 1.099
4h2u ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.909
3mey ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.880
4bwa N0BPyrrolysine--tRNA ligase / 0.798
2q7h YLYPyrrolysine--tRNA ligase / 0.791
3vqv ANPPyrrolysine--tRNA ligase / 0.783
3a5z KAAElongation factor P--(R)-beta-lysine ligase / 0.772
4xeo A5AAlanine--tRNA ligase, cytoplasmic / 0.758
4bw9 ANPPyrrolysine--tRNA ligase / 0.748
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.746
3bju ATPLysine--tRNA ligase 6.1.1.6 0.742
1nj5 P5AProline--tRNA ligase / 0.727
1nj6 A5AProline--tRNA ligase / 0.720
1c0a AMOAspartate--tRNA ligase / 0.719
3e9i XAHLysine--tRNA ligase 6.1.1.6 0.717
2x86 ADPADP-L-glycero-D-manno-heptose-6-epimerase / 0.711
3e9h KAALysine--tRNA ligase 6.1.1.6 0.708
1b7y FYAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.695
4h2w 5GPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.693
1fyf SSAThreonine--tRNA ligase 6.1.1.3 0.684
2zio AYBPyrrolysine--tRNA ligase / 0.679
2zdg ADPD-alanine--D-alanine ligase / 0.665
3ehj ACPSensor histidine kinase DesK 2.7.13.3 0.662
2o8b ADPDNA mismatch repair protein Msh2 / 0.661
2zt7 ATPGlycine--tRNA ligase / 0.656
4jqe ANPCasein kinase II subunit alpha 2.7.11.1 0.656