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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
1r6t TYM Tryptophan--tRNA ligase, cytoplasmic 6.1.1.2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1r6t TYMTryptophan--tRNA ligase, cytoplasmic 6.1.1.2 1.395
3kt3 TYMTryptophan--tRNA ligase, cytoplasmic 6.1.1.2 1.238
3jxe TYMTryptophan--tRNA ligase / 1.028
1r6u TYMTryptophan--tRNA ligase, cytoplasmic 6.1.1.2 1.020
4j75 TYMTryptophan--tRNA ligase / 0.946
2quj TYMTryptophan--tRNA ligase, cytoplasmic 6.1.1.2 0.910
3kt8 LTNTryptophan--tRNA ligase, cytoplasmic 6.1.1.2 0.823
1i6l TYMTryptophan--tRNA ligase 6.1.1.2 0.729
1i6k TYMTryptophan--tRNA ligase 6.1.1.2 0.728
3ag6 PAJPantothenate synthetase / 0.693
3akz GSUGlutamate--tRNA ligase 2 / 0.687
4ys0 ADPProtein translocase subunit SecA / 0.677
3coz 54HPantothenate synthetase 6.3.2.1 0.676
3kh5 ADPUncharacterized protein MJ1225 / 0.668
4lv8 ADPRhoptry protein 5 C / 0.662
4zse ANPEpidermal growth factor receptor 2.7.10.1 0.661
1p9b IMOAdenylosuccinate synthetase / 0.660
3iwj NADAminoaldehyde dehydrogenase / 0.658
3ea0 ATPATPase, ParA family / 0.657
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.656
2wme NAPNAD/NADP-dependent betaine aldehyde dehydrogenase / 0.656
4lv5 ADPRhoptry protein 5B / 0.654
1w5s ADPORC1-type DNA replication protein 2 / 0.651
1lny IMOAdenylosuccinate synthetase isozyme 1 / 0.650