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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
3qwp SAM Histone-lysine N-methyltransferase SMYD3 2.1.1.43

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3qwp SAMHistone-lysine N-methyltransferase SMYD3 2.1.1.43 1.098
5hq8 SAHHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.983
3pdn SFGHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.981
3ru0 SFGHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.912
3oxf SAHHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.905
3tg4 SAMN-lysine methyltransferase SMYD2 / 0.903
5ex0 SAHHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.880
2h21 SAMRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic 2.1.1.127 0.850
4o6f SAHN-lysine methyltransferase SMYD2 / 0.843
5jhn SAMHistone-lysine N-methyltransferase EHMT2 / 0.808
5jin SAMHistone-lysine N-methyltransferase EHMT2 / 0.808
4j83 SAMHistone-lysine N-methyltransferase SETD7 2.1.1.43 0.805
1n6c SAMHistone-lysine N-methyltransferase SETD7 2.1.1.43 0.803
3n71 SFGHistone-lysine N-methyltransferase Smyd1 / 0.794
3rib SAHN-lysine methyltransferase SMYD2 / 0.792
5jj0 SAMHistone-lysine N-methyltransferase EHMT2 / 0.792
2r3a SAMHistone-lysine N-methyltransferase SUV39H2 2.1.1.43 0.786
3ooi SAMHistone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific 2.1.1.43 0.785
5czy SAMEukaryotic huntingtin interacting protein B / 0.778
4o30 SAHProbable Histone-lysine N-methyltransferase ATXR5 2.1.1.43 0.777
3fpd SAHHistone-lysine N-methyltransferase EHMT1 / 0.771
2igq SAHHistone-lysine N-methyltransferase EHMT1 / 0.766
1mlv SAHRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic 2.1.1.127 0.760
4qen SAHHistone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 2.1.1.43 0.760
3hna SAHHistone-lysine N-methyltransferase EHMT1 / 0.759
3m53 SAHHistone-lysine N-methyltransferase SETD7 2.1.1.43 0.759
1ozv SAHRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic 2.1.1.127 0.757
2rfi SAHHistone-lysine N-methyltransferase EHMT1 / 0.756
3kmt SAHHistone H3K27 methylase / 0.752
3cbp SFGHistone-lysine N-methyltransferase SETD7 2.1.1.43 0.746
3swc SAHHistone-lysine N-methyltransferase EHMT1 / 0.744
1p0y SAHRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic 2.1.1.127 0.730
2h23 SAHRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic 2.1.1.127 0.729
2o8j SAHHistone-lysine N-methyltransferase EHMT2 / 0.729
4bup SAMHistone-lysine N-methyltransferase KMT5B 2.1.1.43 0.711
5f59 SAHHistone-lysine N-methyltransferase 2C 2.1.1.43 0.711
2bqz SAHN-lysine methyltransferase KMT5A / 0.707
3s8p SAMHistone-lysine N-methyltransferase KMT5B 2.1.1.43 0.706
4z4p SAHHistone-lysine N-methyltransferase 2D 2.1.1.43 0.703
3rv4 ADPBiotin carboxylase 6.3.4.14 0.689
2h2j SFGRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic 2.1.1.127 0.685
4ynm SAMHistone-lysine N-methyltransferase ASH1L 2.1.1.43 0.685
3tw6 ADPPyruvate carboxylase / 0.678
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.675
5hyn SAHHistone-lysine N-methyltransferase EZH2 2.1.1.43 0.675
4jlp ADPAdenylate kinase / 0.671
2j9g ADPBiotin carboxylase 6.3.4.14 0.664
4r1l ADPPhenylacetate-coenzyme A ligase / 0.662
1olt SAMOxygen-independent coproporphyrinogen III oxidase / 0.661
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 0.659
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.656
4kgn SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.656