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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
4bwa N0B Pyrrolysine--tRNA ligase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4bwa N0BPyrrolysine--tRNA ligase / 1.262
2q7h YLYPyrrolysine--tRNA ligase / 0.999
3pzc GAPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.798
1c0a AMOAspartate--tRNA ligase / 0.782
3a5z KAAElongation factor P--(R)-beta-lysine ligase / 0.779
4xeo A5AAlanine--tRNA ligase, cytoplasmic / 0.778
3vqx BLKPyrrolysine--tRNA ligase / 0.774
2i4m PSDProline--tRNA ligase 6.1.1.15 0.733
1fyf SSAThreonine--tRNA ligase 6.1.1.3 0.722
3e9h KAALysine--tRNA ligase 6.1.1.6 0.722
1b7y FYAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.716
4bw9 ANPPyrrolysine--tRNA ligase / 0.705
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.697
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.695
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.692
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.691
2aly YSAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.690
3m4p 4ADAsparaginyl-tRNA synthetase, putative / 0.686
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.681
4h2u ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.681
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.680
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.680
3vqv ANPPyrrolysine--tRNA ligase / 0.674
2zt5 B4PGlycine--tRNA ligase / 0.673
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.670
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.668
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.666
1nj5 P5AProline--tRNA ligase / 0.664
2x86 ADPADP-L-glycero-D-manno-heptose-6-epimerase / 0.663
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.663
5ce3 ADPProtein kinase YopO / 0.663
4ffl ADPUncharacterized protein / 0.661
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.661
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.659
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.658
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.657
3mey ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.654
4xfj ANPArgininosuccinate synthase / 0.654
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.652
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.651
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.650
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.650