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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
4xba 5GP Aprataxin-like protein 3

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4xba 5GPAprataxin-like protein 3 0.927
4xba GMPAprataxin-like protein 3 0.726
1xmm M7Gm7GpppX diphosphatase 3.6.1.59 0.718
3n1t 5GPPurine nucleoside phosphoramidase / 0.707
3ldg SAHUncharacterized protein / 0.683
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.682
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.671
1st0 GTGm7GpppX diphosphatase 3.6.1.59 0.670
2gsd NADFormate dehydrogenase / 0.670
5bv3 M7Gm7GpppX diphosphatase 3.6.1.59 0.670
4egu 5GPPutative histidine triad (HIT) protein / 0.662
3f46 I2C5,10-methenyltetrahydromethanopterin hydrogenase 1.12.98.2 0.656
5i2f BS5Histidine triad nucleotide-binding protein 1 3 0.656
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.655
5f8f SFGPossible transcriptional regulatory protein / 0.653
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.652
2nad NADFormate dehydrogenase / 0.652
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.650
3fri SAH16S rRNA methylase / 0.650