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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
4bw9 ANP Pyrrolysine--tRNA ligase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4bw9 ANPPyrrolysine--tRNA ligase / 1.264
3vqv ANPPyrrolysine--tRNA ligase / 1.148
3bju ATPLysine--tRNA ligase 6.1.1.6 0.946
2q7h YLYPyrrolysine--tRNA ligase / 0.857
1fyf SSAThreonine--tRNA ligase 6.1.1.3 0.823
3e9h KAALysine--tRNA ligase 6.1.1.6 0.818
2zio AYBPyrrolysine--tRNA ligase / 0.790
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.782
1nj6 A5AProline--tRNA ligase / 0.774
3mey ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.771
4h2u ATPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.770
3e9i XAHLysine--tRNA ligase 6.1.1.6 0.765
3a5z KAAElongation factor P--(R)-beta-lysine ligase / 0.762
3pzc GAPAmino acid--[acyl-carrier-protein] ligase 1 6.2.1.n2 0.748
2zt5 B4PGlycine--tRNA ligase / 0.741
1nj5 P5AProline--tRNA ligase / 0.740
1c0a AMOAspartate--tRNA ligase / 0.731
3m4p 4ADAsparaginyl-tRNA synthetase, putative / 0.714
4bwa N0BPyrrolysine--tRNA ligase / 0.705
3ufg ATPGlycine--tRNA ligase alpha subunit / 0.700
4xeo A5AAlanine--tRNA ligase, cytoplasmic / 0.692
4bup SAMHistone-lysine N-methyltransferase KMT5B 2.1.1.43 0.690
2i4n 5CAProline--tRNA ligase 6.1.1.15 0.683
2zt7 ATPGlycine--tRNA ligase / 0.683
2x86 ADPADP-L-glycero-D-manno-heptose-6-epimerase / 0.680
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.680
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.680
1b7y FYAPhenylalanine--tRNA ligase alpha subunit 6.1.1.20 0.676
1s16 ANPDNA topoisomerase 4 subunit B / 0.675
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.671
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.669
2ydo ADNAdenosine receptor A2a / 0.664
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.661
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.660
1bxr ANPCarbamoyl-phosphate synthase large chain / 0.657
4xlv ACPInsulin receptor 2.7.10.1 0.657
4ffl ADPUncharacterized protein / 0.655
2dsi SAHDiphthine synthase / 0.653
2ek4 SAHDiphthine synthase / 0.653
2zbv ADNUncharacterized protein / 0.651
2p5c SAHDiphthine synthase / 0.650