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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
5dto SAH Genome polyprotein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5dto SAHGenome polyprotein / 0.912
5jjs SAHGenome polyprotein / 0.816
3eld SFGMethyltransferase / 0.778
3p97 SAMGenome polyprotein 2.1.1.56 0.770
5jjr SAHGenome polyprotein / 0.768
3eva SAHGenome polyprotein 2.1.1.56 0.762
3evc SAHGenome polyprotein 2.1.1.56 0.762
4ctk SAMGenome polyprotein / 0.760
3lkz SFGGenome polyprotein / 0.753
4ctj SAMGenome polyprotein / 0.752
1r6a SAHGenome polyprotein 2.7.7.48 0.746
2px2 SAHGenome polyprotein 2.7.7.48 0.741
3evb SAHGenome polyprotein 2.1.1.56 0.741
3p8z SAHGenome polyprotein 2.1.1.56 0.741
4k6m SAHGenome polyprotein / 0.736
3p8z 36AGenome polyprotein 2.1.1.56 0.724
3emd SFGMethyltransferase / 0.721
2p3q SAHGenome polyprotein / 0.720
2p41 SAHGenome polyprotein / 0.720
2wa2 SAMGenome polyprotein / 0.719
3elu SAMMethyltransferase / 0.717
2px5 SAHGenome polyprotein 2.7.7.48 0.714
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.711
3ely SAHMethyltransferase / 0.701
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.698
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.697
2oy0 SAHGenome polyprotein / 0.696
1yf3 SAHDNA adenine methylase / 0.694
3tos SAHCalS11 / 0.693
2p1d SAHGenome polyprotein 2.7.7.48 0.691
3c3y SAHO-methyltransferase / 0.685
2pxa SAHGenome polyprotein 2.7.7.48 0.683
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.681
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.677
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.677
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.675
4uck SAMLarge structural protein / 0.672
3vyw SAMUncharacterized protein / 0.671
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.670
1nw5 SAMModification methylase RsrI 2.1.1.72 0.667
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.667
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.666
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.660
4dmg SAMUncharacterized protein / 0.657
2plw SAMRibosomal RNA methyltransferase, putative / 0.656
2xbm SAHGenome polyprotein / 0.652