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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
5ex0SAHHistone-lysine N-methyltransferase SMYD32.1.1.43

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
5ex0SAHHistone-lysine N-methyltransferase SMYD32.1.1.431.000
3ru0SFGHistone-lysine N-methyltransferase SMYD32.1.1.430.637
3oxfSAHHistone-lysine N-methyltransferase SMYD32.1.1.430.616
3pdnSFGHistone-lysine N-methyltransferase SMYD32.1.1.430.593
5hq8SAHHistone-lysine N-methyltransferase SMYD32.1.1.430.589
3qwpSAMHistone-lysine N-methyltransferase SMYD32.1.1.430.588
3tg4SAMN-lysine methyltransferase SMYD2/0.550
4o6fSAHN-lysine methyltransferase SMYD2/0.527
3ribSAHN-lysine methyltransferase SMYD2/0.512
3n71SFGHistone-lysine N-methyltransferase Smyd1/0.495
1mlvSAHRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.484
2h2eSA8Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.468
4dc0NDPPutative ketoacyl reductase1.3.10.455
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
1ozvSAHRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.448
3qgf46FGenome polyprotein2.7.7.480.446
5jinSAMHistone-lysine N-methyltransferase EHMT2/0.444
3cbpSFGHistone-lysine N-methyltransferase SETD72.1.1.430.443
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4b68NAPL-ornithine N(5)-monooxygenase/0.443
3m53SAHHistone-lysine N-methyltransferase SETD72.1.1.430.441
4yfy0FXVioF/0.441
5jj0SAMHistone-lysine N-methyltransferase EHMT2/0.441
3adaNADSubunit alpha of sarocosine oxidase/0.440