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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
10mh SAH Modification methylase HhaI 2.1.1.37

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
10mh SAHModification methylase HhaI 2.1.1.37 0.987
9mht SAHModification methylase HhaI 2.1.1.37 0.929
2uyh SAHModification methylase HhaI 2.1.1.37 0.916
1skm SAHModification methylase HhaI 2.1.1.37 0.903
7mht SAHModification methylase HhaI 2.1.1.37 0.886
5mht SAHModification methylase HhaI 2.1.1.37 0.883
2c7q SAHModification methylase HhaI 2.1.1.37 0.875
3mht SAHModification methylase HhaI 2.1.1.37 0.871
4mht SAHModification methylase HhaI 2.1.1.37 0.866
2z6u SAHModification methylase HhaI 2.1.1.37 0.841
8mht SAHModification methylase HhaI 2.1.1.37 0.836
1mht SAHModification methylase HhaI 2.1.1.37 0.834
2zcj SAHModification methylase HhaI 2.1.1.37 0.810
2i9k SAHModification methylase HhaI 2.1.1.37 0.805
4dkj SAHCytosine-specific methyltransferase / 0.788
1fjx SAHModification methylase HhaI 2.1.1.37 0.784
3qv2 SAH5-cytosine DNA methyltransferase / 0.769
3tm4 SAMUncharacterized protein / 0.752
4rtk SAHDNA adenine methylase 2.1.1.72 0.741
3ldg SAHUncharacterized protein / 0.734
2hmy SAMModification methylase HhaI 2.1.1.37 0.730
1nw5 SAMModification methylase RsrI 2.1.1.72 0.729
1g60 SAMModification methylase MboII 2.1.1.72 0.728
1boo SAHModification methylase PvuII 2.1.1.113 0.721
4h0n SAHDnmt2 / 0.720
3c3y SAHO-methyltransferase / 0.718
2zif SAMMethyltransferase / 0.716
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.716
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.715
4nec SAHPutative SAM-dependent methyltransferase / 0.714
2g1p SAHDNA adenine methylase 2.1.1.72 0.713
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.712
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.708
4dmg SAMUncharacterized protein / 0.707
1yf3 SAHDNA adenine methylase / 0.704
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.704
2cww SAHUncharacterized protein / 0.702
4rtj SFGDNA adenine methylase 2.1.1.72 0.702
1nw6 SFGModification methylase RsrI 2.1.1.72 0.701
3go4 SAHUncharacterized protein / 0.701
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.701
2br5 SAHCephalosporin hydroxylase CmcI / 0.698
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.696
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.696
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.696
2px2 SAHGenome polyprotein 2.7.7.48 0.695
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.695
4gbe SAHDNA adenine methylase 2.1.1.72 0.695
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.692
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.691
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.689
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.689
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.688
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.688
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.688
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.688
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.687
1r6a SAHGenome polyprotein 2.7.7.48 0.686
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.686
5bp9 SAHPutative methyltransferase protein / 0.686
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.685
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.685
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.684
4poo SAMPutative RNA methylase / 0.683
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.682
3e23 SAMUncharacterized protein / 0.681
2hmv ADPKtr system potassium uptake protein A / 0.680
1eg2 MTAModification methylase RsrI 2.1.1.72 0.679
4rtm SAMDNA adenine methylase 2.1.1.72 0.679
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.678
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.678
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.677
4hh4 SAHCcbJ / 0.677
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.677
4rts SAMDNA adenine methylase 2.1.1.72 0.677
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.677
2np6 NEAModification methylase TaqI 2.1.1.72 0.675
3ldf SAHUncharacterized protein / 0.675
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.674
2qe6 SAMUncharacterized protein / 0.674
3emd SFGMethyltransferase / 0.674
4rto SFGDNA adenine methylase 2.1.1.72 0.674
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.673
2ore SAHDNA adenine methylase 2.1.1.72 0.673
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.673
3fpf MTAUncharacterized protein / 0.673
2o07 MTASpermidine synthase 2.5.1.16 0.672
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.672
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.672
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.672
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.672
4rtl SFGDNA adenine methylase 2.1.1.72 0.672
4k6m SAHGenome polyprotein / 0.671
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.671
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.671
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.671
3eey SAMrRNA methylase / 0.670
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.670
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.670
2pxa SAHGenome polyprotein 2.7.7.48 0.669
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.669
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.669
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.669
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.668
3p8z SAHGenome polyprotein 2.1.1.56 0.666
3tr6 SAHO-methyltransferase / 0.666
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.666
2px5 SAHGenome polyprotein 2.7.7.48 0.665
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.665
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.665
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.664
2eg5 SAH7-methylxanthosine synthase 1 / 0.664
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.664
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.663
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.662
4ft4 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.662
1g1a NADdTDP-glucose 4,6-dehydratase / 0.660
1nhr FADNADH peroxidase 1.11.1.1 0.660
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.660
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.659
1nhq FADNADH peroxidase 1.11.1.1 0.659
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.659
2yqz SAMUncharacterized protein / 0.658
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.657
3tos SAHCalS11 / 0.657
2yxl SFG450aa long hypothetical fmu protein / 0.656
3ely SAHMethyltransferase / 0.656
3tm5 SFGUncharacterized protein / 0.656
2o06 MTASpermidine synthase 2.5.1.16 0.655
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.655
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.655
2f8l SAMLmo1582 protein / 0.654
3cbg SAHO-methyltransferase / 0.654
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.654
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.653
2p3q SAHGenome polyprotein / 0.653
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.653
3tlj SAHUncharacterized protein / 0.653
4c03 SFGProtein arginine N-methyltransferase 6 / 0.653
4rtn SAHDNA adenine methylase 2.1.1.72 0.653
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.652
3eld SFGMethyltransferase / 0.652
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.652
1npx FADNADH peroxidase 1.11.1.1 0.651
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.651
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.651
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.651
2plw SAMRibosomal RNA methyltransferase, putative / 0.650
2wa2 SAMGenome polyprotein / 0.650