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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
4x7y SAH Mycinamicin III 3''-O-methyltransferase 2.1.1.237

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 1.110
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 1.099
3tos SAHCalS11 / 0.888
4gf5 SAHCalS11 / 0.817
3c3y SAHO-methyltransferase / 0.797
4dmg SAMUncharacterized protein / 0.787
3cbg SAHO-methyltransferase / 0.779
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.740
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.734
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.734
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.734
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.731
3vyw SAMUncharacterized protein / 0.731
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.730
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.727
2plw SAMRibosomal RNA methyltransferase, putative / 0.723
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.720
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.717
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.716
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.713
4kwc SAHMethyltransferase domain family / 0.713
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.712
4ctk SAMGenome polyprotein / 0.712
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.712
5eku SAHArginine N-methyltransferase, putative / 0.709
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.708
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.708
4kvz SAHPtnL protein / 0.708
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.707
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.706
1nw5 SAMModification methylase RsrI 2.1.1.72 0.703
1yf3 SAHDNA adenine methylase / 0.703
4oa5 SAHO-methyltransferase family protein / 0.702
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.702
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.701
3emd SFGMethyltransferase / 0.700
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.700
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.699
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.699
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.699
4k6m SAHGenome polyprotein / 0.698
5dto SAHGenome polyprotein / 0.698
4ctj SAMGenome polyprotein / 0.697
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.696
3lkz SFGGenome polyprotein / 0.695
3p97 SAMGenome polyprotein 2.1.1.56 0.695
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.694
3duw SAHO-methyltransferase, putative / 0.693
1y9d FADPyruvate oxidase 1.2.3.3 0.692
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.691
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.691
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.688
3eva SAHGenome polyprotein 2.1.1.56 0.687
3evc SAHGenome polyprotein 2.1.1.56 0.686
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.686
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.686
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.685
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.685
2bm9 SAMCephalosporin hydroxylase CmcI / 0.684
2gs9 SAHUncharacterized protein / 0.684
2px5 SAHGenome polyprotein 2.7.7.48 0.683
3evb SAHGenome polyprotein 2.1.1.56 0.683
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.682
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.682
3eld SFGMethyltransferase / 0.682
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.682
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.682
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.681
3go4 SAHUncharacterized protein / 0.681
3mj4 FADUDP-galactopyranose mutase / 0.681
3nn6 FB06-hydroxy-L-nicotine oxidase / 0.681
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.681
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.681
5je4 SAHMethyl transferase / 0.681
2br5 SAHCephalosporin hydroxylase CmcI / 0.680
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.680
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.679
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.679
3kkz SAMUncharacterized protein / 0.679
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.678
5jdz SAHMethyl transferase / 0.678
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.677
4c03 SFGProtein arginine N-methyltransferase 6 / 0.677
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.676
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.676
5jjr SAHGenome polyprotein / 0.676
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.675
3hvk 719Catechol O-methyltransferase 2.1.1.6 0.675
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.674
3p8z SAHGenome polyprotein 2.1.1.56 0.674
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.673
3p8z 36AGenome polyprotein 2.1.1.56 0.673
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.672
1l9k SAHGenome polyprotein 2.7.7.48 0.672
3tr6 SAHO-methyltransferase / 0.672
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.672
3fri SAH16S rRNA methylase / 0.671
4lwp SAHArginine N-methyltransferase, putative / 0.671
2p41 SAHGenome polyprotein / 0.670
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.670
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.670
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.669
2cww SAHUncharacterized protein / 0.669
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.669
4guu FA9Lysine-specific histone demethylase 1B 1 0.669
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.669
2p35 SAHTrans-aconitate 2-methyltransferase / 0.668
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.667
1r6a SAHGenome polyprotein 2.7.7.48 0.666
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.666
5epe SAHUncharacterized protein / 0.666
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.665
3fpf MTAUncharacterized protein / 0.664
5je3 SAHMethyl transferase / 0.664
2yxl SFG450aa long hypothetical fmu protein / 0.662
4yac NAIC alpha-dehydrogenase / 0.662
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.659
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.659
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.659
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.659
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.657
2pxa SAHGenome polyprotein 2.7.7.48 0.657
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.657
3t7s SAMUncharacterized protein / 0.657
5bp9 SAHPutative methyltransferase protein / 0.657
1f3l SAHProtein arginine N-methyltransferase 3 / 0.656
1g60 SAMModification methylase MboII 2.1.1.72 0.656
2wa2 SAMGenome polyprotein / 0.656
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.656
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.656
2hnk SAHSAM-dependent O-methyltransferase / 0.654
3bwc SAMSpermidine synthase, putative / 0.654
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.653
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.653
4rtj SFGDNA adenine methylase 2.1.1.72 0.653
2eq7 NADDihydrolipoyl dehydrogenase / 0.652
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.652
3elu SAMMethyltransferase / 0.652
1ty8 ADPProbable ADP-ribose 1''-phosphate phosphatase YML087W 3.1.3.84 0.651
1v59 NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.651
3p9k SAHCaffeic acid O-methyltransferase / 0.651
4yuz S4MSpermidine synthase, putative / 0.651
3dh0 SAMUncharacterized protein / 0.650
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.650