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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
5bv3 M7G m7GpppX diphosphatase 3.6.1.59

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5bv3 M7Gm7GpppX diphosphatase 3.6.1.59 1.277
1xmm M7Gm7GpppX diphosphatase 3.6.1.59 0.919
1st0 GTGm7GpppX diphosphatase 3.6.1.59 0.860
4egu 5GPPutative histidine triad (HIT) protein / 0.697
3n1s 5GPPurine nucleoside phosphoramidase / 0.687
4xba 5GPAprataxin-like protein 3 0.670
3oxk 5GPHistidine triad nucleotide-binding protein 3 0.667
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.661
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.656
4kqs IPEFarnesyl pyrophosphate synthase 2.5.1.10 0.654