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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
3rib SAH N-lysine methyltransferase SMYD2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3rib SAHN-lysine methyltransferase SMYD2 / 1.062
4o6f SAHN-lysine methyltransferase SMYD2 / 0.825
3pdn SFGHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.805
3tg4 SAMN-lysine methyltransferase SMYD2 / 0.793
3qwp SAMHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.792
3n71 SFGHistone-lysine N-methyltransferase Smyd1 / 0.788
5ex0 SAHHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.766
3ru0 SFGHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.755
5hq8 SAHHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.754
3oxf SAHHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.743
4j83 SAMHistone-lysine N-methyltransferase SETD7 2.1.1.43 0.707
3m53 SAHHistone-lysine N-methyltransferase SETD7 2.1.1.43 0.696
3cbp SFGHistone-lysine N-methyltransferase SETD7 2.1.1.43 0.693
1n6c SAMHistone-lysine N-methyltransferase SETD7 2.1.1.43 0.681
2rd5 NLGAcetylglutamate kinase, chloroplastic 2.7.2.8 0.676
2h21 SAMRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic 2.1.1.127 0.674
3zzh NLGProtein ARG5,6, mitochondrial 2.7.2.8 0.670
4h12 SAHHistone-lysine N-methyltransferase SETD2 2.1.1.43 0.669
4ypa SAMHistone-lysine N-methyltransferase ASH1L 2.1.1.43 0.667
4qen SAHHistone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 2.1.1.43 0.666
1ozv SAHRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic 2.1.1.127 0.665
1u5a BIKL-lactate dehydrogenase 1.1.1.27 0.665
3zno SE5D-amino-acid oxidase 1.4.3.3 0.663
1mlv SAHRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic 2.1.1.127 0.657
2qs4 LY5Glutamate receptor ionotropic, kainate 1 / 0.657
5bp9 SAHPutative methyltransferase protein / 0.657
3zzf NLGProtein ARG5,6, mitochondrial 2.7.2.8 0.656
2rfi SAHHistone-lysine N-methyltransferase EHMT1 / 0.654
4o30 SAHProbable Histone-lysine N-methyltransferase ATXR5 2.1.1.43 0.653
1p0y SAHRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic 2.1.1.127 0.652
3tw6 ADPPyruvate carboxylase / 0.652
2h23 SAHRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic 2.1.1.127 0.651
2bqz SAHN-lysine methyltransferase KMT5A / 0.650