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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
3mey 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
3mey ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 1.335
4h2u ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.881
3pzc GAPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.880
3bju ATPLysine--tRNA ligase 6.1.1.6 0.801
4bw9 ANPPyrrolysine--tRNA ligase / 0.771
1fyf SSAThreonine--tRNA ligase 6.1.1.3 0.768
3vqv ANPPyrrolysine--tRNA ligase / 0.763
3e9i XAHLysine--tRNA ligase 6.1.1.6 0.760
3e9h KAALysine--tRNA ligase 6.1.1.6 0.759
3a5z KAAElongation factor P--(R)-beta-lysine ligase / 0.748
2q7h YLYPyrrolysine--tRNA ligase / 0.741
1nj6 A5AProline--tRNA ligase / 0.726
2zt7 ATPGlycine--tRNA ligase / 0.723
1nj5 P5AProline--tRNA ligase / 0.701
1c0a AMOAspartate--tRNA ligase / 0.698
4h2w 5GPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.696
2zt5 B4PGlycine--tRNA ligase / 0.688
2aly YSAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.684
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.677
1b7y FYAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.669
2x86 ADPADP-L-glycero-D-manno-heptose-6-epimerase / 0.664
4xeo A5AAlanine--tRNA ligase, cytoplasmic / 0.664
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.659
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.655
4bwa N0BPyrrolysine--tRNA ligase / 0.654
3m4p 4ADAsparaginyl-tRNA synthetase, putative / 0.653
1s16 ANPDNA topoisomerase 4 subunit B / 0.652
4bup SAMHistone-lysine N-methyltransferase KMT5B 2.1.1.43 0.650