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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
3a5y KAA Elongation factor P--(R)-beta-lysine ligase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 1.338
3a5z KAAElongation factor P--(R)-beta-lysine ligase / 1.121
3e9h KAALysine--tRNA ligase 6.1.1.6 0.944
3vqv ANPPyrrolysine--tRNA ligase / 0.839
1c0a AMOAspartate--tRNA ligase / 0.828
4bw9 ANPPyrrolysine--tRNA ligase / 0.782
1fyf SSAThreonine--tRNA ligase 6.1.1.3 0.777
1nj5 P5AProline--tRNA ligase / 0.758
3pzc GAPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.746
1ses AHXSerine--tRNA ligase 6.1.1.11 0.729
1nj6 A5AProline--tRNA ligase / 0.726
2q7h YLYPyrrolysine--tRNA ligase / 0.722
3bju ATPLysine--tRNA ligase 6.1.1.6 0.718
3m4p 4ADAsparaginyl-tRNA synthetase, putative / 0.703
2p0a ANPSynapsin-3 / 0.698
2zio AYBPyrrolysine--tRNA ligase / 0.695
4bwa N0BPyrrolysine--tRNA ligase / 0.694
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.687
4ffl ADPUncharacterized protein / 0.682
3mey ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.677
3vqx BLKPyrrolysine--tRNA ligase / 0.677
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.672
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.671
4h2u ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.671
4zol ACPTubulin tyrosine ligase / 0.670
3r5f ATPD-alanine--D-alanine ligase / 0.669
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.668
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.668
2i4m PSDProline--tRNA ligase 6.1.1.15 0.665
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.665
4s1b 2BALmo1466 protein / 0.665
2x86 ADPADP-L-glycero-D-manno-heptose-6-epimerase / 0.662
2aly YSAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.659
3lfz ADPUncharacterized protein MJ1225 / 0.659
4xeo A5AAlanine--tRNA ligase, cytoplasmic / 0.656
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.651
4prx ADPDNA gyrase subunit B / 0.651
2dy9 ADPNucleoside diphosphate kinase 2.7.4.6 0.650