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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
5k7w SAH N6-adenosine-methyltransferase 70 kDa subunit

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 1.106
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.932
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.931
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.877
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.753
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.753
3ely SAHMethyltransferase / 0.752
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.747
1yf3 SAHDNA adenine methylase / 0.741
4k6m SAHGenome polyprotein / 0.732
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.728
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.727
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.727
1boo SAHModification methylase PvuII 2.1.1.113 0.726
2px2 SAHGenome polyprotein 2.7.7.48 0.724
3eld SFGMethyltransferase / 0.724
2cww SAHUncharacterized protein / 0.722
1nw5 SAMModification methylase RsrI 2.1.1.72 0.718
1r6a SAHGenome polyprotein 2.7.7.48 0.716
2g1p SAHDNA adenine methylase 2.1.1.72 0.715
2wa2 SAMGenome polyprotein / 0.715
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.713
3duw SAHO-methyltransferase, putative / 0.713
3ldf SAHUncharacterized protein / 0.712
3p8z SAHGenome polyprotein 2.1.1.56 0.711
3tos SAHCalS11 / 0.710
3p97 SAMGenome polyprotein 2.1.1.56 0.708
3c3y SAHO-methyltransferase / 0.707
2p41 SAHGenome polyprotein / 0.704
4oa5 SAHO-methyltransferase family protein / 0.702
2z6u SAHModification methylase HhaI 2.1.1.37 0.701
3emd SFGMethyltransferase / 0.700
2c7q SAHModification methylase HhaI 2.1.1.37 0.699
2p3q SAHGenome polyprotein / 0.699
3evb SAHGenome polyprotein 2.1.1.56 0.698
2px5 SAHGenome polyprotein 2.7.7.48 0.697
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.696
4ctj SAMGenome polyprotein / 0.694
4ctk SAMGenome polyprotein / 0.692
3evg SAHGenome polyprotein 2.1.1.56 0.691
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.689
4uck SAMLarge structural protein / 0.688
3elu SAMMethyltransferase / 0.687
1fjx SAHModification methylase HhaI 2.1.1.37 0.685
3ou2 SAHSAM-dependent methyltransferase / 0.685
2yxl SFG450aa long hypothetical fmu protein / 0.684
5jjr SAHGenome polyprotein / 0.684
2zif SAMMethyltransferase / 0.683
4gf5 SAHCalS11 / 0.681
3eva SAHGenome polyprotein 2.1.1.56 0.679
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.678
2p1d SAHGenome polyprotein 2.7.7.48 0.677
1l9k SAHGenome polyprotein 2.7.7.48 0.676
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.675
1skm SAHModification methylase HhaI 2.1.1.37 0.675
2eg5 SAH7-methylxanthosine synthase 1 / 0.675
2zcj SAHModification methylase HhaI 2.1.1.37 0.675
4gbe SAHDNA adenine methylase 2.1.1.72 0.674
2br5 SAHCephalosporin hydroxylase CmcI / 0.673
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.673
3lkz SFGGenome polyprotein / 0.672
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.672
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.671
2uyh SAHModification methylase HhaI 2.1.1.37 0.671
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.671
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.670
4poo SAMPutative RNA methylase / 0.670
5d4v SAHUncharacterized protein MJ0489 / 0.670
10mh SAHModification methylase HhaI 2.1.1.37 0.669
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.668
2i9k SAHModification methylase HhaI 2.1.1.37 0.667
3mht SAHModification methylase HhaI 2.1.1.37 0.667
4dkj SAHCytosine-specific methyltransferase / 0.667
4nec SAHPutative SAM-dependent methyltransferase / 0.667
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.667
5f2k SAHUncharacterized protein / 0.666
3evc SAHGenome polyprotein 2.1.1.56 0.665
5d4u SAMUncharacterized protein MJ0489 / 0.665
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.664
3lcc SAHThiocyanate methyltransferase 1 / 0.662
3cbg SAHO-methyltransferase / 0.661
1mht SAHModification methylase HhaI 2.1.1.37 0.658
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.658
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.658
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.657
2yqz SAMUncharacterized protein / 0.656
5a8e XTKBeta-1 adrenergic receptor / 0.656
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.655
2hnk SAHSAM-dependent O-methyltransferase / 0.654
2pxa SAHGenome polyprotein 2.7.7.48 0.654
3rw9 DSHSpermidine synthase 2.5.1.16 0.654
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.651
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.650
5je4 SAHMethyl transferase / 0.650
3nya JTZBeta-2 adrenergic receptor / 0.650