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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
5k7u SAM N6-adenosine-methyltransferase 70 kDa subunit

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 1.136
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.931
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.897
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.853
1nw5 SAMModification methylase RsrI 2.1.1.72 0.819
1yf3 SAHDNA adenine methylase / 0.802
2g1p SAHDNA adenine methylase 2.1.1.72 0.784
3c3y SAHO-methyltransferase / 0.766
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.761
2cww SAHUncharacterized protein / 0.749
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.744
3tos SAHCalS11 / 0.735
2px5 SAHGenome polyprotein 2.7.7.48 0.734
3evb SAHGenome polyprotein 2.1.1.56 0.723
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.719
1boo SAHModification methylase PvuII 2.1.1.113 0.717
3emd SFGMethyltransferase / 0.716
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.716
1g60 SAMModification methylase MboII 2.1.1.72 0.714
2p3q SAHGenome polyprotein / 0.713
3eva SAHGenome polyprotein 2.1.1.56 0.708
4rtj SFGDNA adenine methylase 2.1.1.72 0.707
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.707
1r6a SAHGenome polyprotein 2.7.7.48 0.706
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.704
4dmg SAMUncharacterized protein / 0.700
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.700
4ctj SAMGenome polyprotein / 0.697
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.697
2px2 SAHGenome polyprotein 2.7.7.48 0.695
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.694
2i9k SAHModification methylase HhaI 2.1.1.37 0.694
2uyh SAHModification methylase HhaI 2.1.1.37 0.694
2wa2 SAMGenome polyprotein / 0.694
3evc SAHGenome polyprotein 2.1.1.56 0.693
3evg SAHGenome polyprotein 2.1.1.56 0.693
3lkz SFGGenome polyprotein / 0.693
3duw SAHO-methyltransferase, putative / 0.692
3ou2 SAHSAM-dependent methyltransferase / 0.692
3p8z SAHGenome polyprotein 2.1.1.56 0.692
4ctk SAMGenome polyprotein / 0.692
3mht SAHModification methylase HhaI 2.1.1.37 0.691
3qv2 SAH5-cytosine DNA methyltransferase / 0.691
1l9k SAHGenome polyprotein 2.7.7.48 0.690
2c7q SAHModification methylase HhaI 2.1.1.37 0.690
3ely SAHMethyltransferase / 0.690
1fjx SAHModification methylase HhaI 2.1.1.37 0.689
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.689
4poo SAMPutative RNA methylase / 0.688
4rtl SFGDNA adenine methylase 2.1.1.72 0.688
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.687
4gbe SAHDNA adenine methylase 2.1.1.72 0.685
4uck SAMLarge structural protein / 0.684
3p97 SAMGenome polyprotein 2.1.1.56 0.682
1nw6 SFGModification methylase RsrI 2.1.1.72 0.681
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.681
3eld SFGMethyltransferase / 0.681
4gf5 SAHCalS11 / 0.681
4k6m SAHGenome polyprotein / 0.681
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.681
2hnk SAHSAM-dependent O-methyltransferase / 0.680
4oa5 SAHO-methyltransferase family protein / 0.680
5jjr SAHGenome polyprotein / 0.679
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.678
4rtk SAHDNA adenine methylase 2.1.1.72 0.678
10mh SAHModification methylase HhaI 2.1.1.37 0.677
5dto SAHGenome polyprotein / 0.677
1skm SAHModification methylase HhaI 2.1.1.37 0.675
2zcj SAHModification methylase HhaI 2.1.1.37 0.674
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.673
5f2k SAHUncharacterized protein / 0.673
3elu SAMMethyltransferase / 0.670
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.669
3cbg SAHO-methyltransferase / 0.668
2z6u SAHModification methylase HhaI 2.1.1.37 0.667
4rtm SAMDNA adenine methylase 2.1.1.72 0.667
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.666
3go4 SAHUncharacterized protein / 0.666
2pxa SAHGenome polyprotein 2.7.7.48 0.664
5d7o AR6NAD-dependent protein deacetylase sirtuin-2 3.5.1 0.664
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.663
2p41 SAHGenome polyprotein / 0.663
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.663
1eg2 MTAModification methylase RsrI 2.1.1.72 0.661
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.661
3eey SAMrRNA methylase / 0.660
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.659
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.659
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.659
3tm4 SAMUncharacterized protein / 0.659
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.659
4c04 SFGProtein arginine N-methyltransferase 6 / 0.657
4h0n SAHDnmt2 / 0.656
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.655
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.655
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.655
4rtq SAHDNA adenine methylase 2.1.1.72 0.655
7mht SAHModification methylase HhaI 2.1.1.37 0.655
9mht SAHModification methylase HhaI 2.1.1.37 0.655
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.651
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.651
2plw SAMRibosomal RNA methyltransferase, putative / 0.650