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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
3go4 SAH Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
3go4 SAHUncharacterized protein / 1.078
5je2 SAHMethyl transferase / 0.851
2qe6 SAMUncharacterized protein / 0.850
5bxy SAHPutative RNA methylase family UPF0020 / 0.802
4lwp SAHArginine N-methyltransferase, putative / 0.801
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.798
3lcc SAHThiocyanate methyltransferase 1 / 0.797
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.796
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.795
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.792
2yqz SAMUncharacterized protein / 0.791
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.777
5je3 SAHMethyl transferase / 0.777
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.774
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.773
1f3l SAHProtein arginine N-methyltransferase 3 / 0.772
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.772
5jdz SAHMethyl transferase / 0.772
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.767
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.761
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.759
5f2k SAHUncharacterized protein / 0.755
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.753
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.753
4kwc SAHMethyltransferase domain family / 0.753
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.753
5bp9 SAHPutative methyltransferase protein / 0.752
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.752
1ori SAHProtein arginine N-methyltransferase 1 / 0.749
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.748
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.747
4kvz SAHPtnL protein / 0.745
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.744
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.743
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.741
1g1a NADdTDP-glucose 4,6-dehydratase / 0.740
2o06 MTASpermidine synthase 2.5.1.16 0.739
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.739
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.738
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.738
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.738
2gs9 SAHUncharacterized protein / 0.737
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.736
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.735
4hh4 SAHCcbJ / 0.734
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.732
2p35 SAHTrans-aconitate 2-methyltransferase / 0.730
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.730
3mht SAHModification methylase HhaI 2.1.1.37 0.728
4nec SAHPutative SAM-dependent methyltransferase / 0.728
4rtk SAHDNA adenine methylase 2.1.1.72 0.726
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.725
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.724
5je4 SAHMethyl transferase / 0.724
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.723
1boo SAHModification methylase PvuII 2.1.1.113 0.722
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.722
1y9d FADPyruvate oxidase 1.2.3.3 0.720
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.720
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.720
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.719
2uyh SAHModification methylase HhaI 2.1.1.37 0.719
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.719
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.719
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.719
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.718
2ore SAHDNA adenine methylase 2.1.1.72 0.718
3t7s SAMUncharacterized protein / 0.718
4qpp SAHProtein arginine N-methyltransferase 6 / 0.718
2eg5 SAH7-methylxanthosine synthase 1 / 0.714
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.712
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.710
4c04 SFGProtein arginine N-methyltransferase 6 / 0.710
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.708
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.707
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.706
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.705
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.702
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.702
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.702
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.702
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.702
10mh SAHModification methylase HhaI 2.1.1.37 0.701
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.701
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.701
4gbe SAHDNA adenine methylase 2.1.1.72 0.701
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.701
4qnv GEKtRNA U34 carboxymethyltransferase / 0.701
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.700
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.700
2hmv ADPKtr system potassium uptake protein A / 0.700
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.700
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.700
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.700
1orh SAHProtein arginine N-methyltransferase 1 / 0.699
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.699
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.698
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.697
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.696
3t7t SAHUncharacterized protein / 0.695
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.694
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.693
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.693
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.692
3kkz SAMUncharacterized protein / 0.692
3ldg SAHUncharacterized protein / 0.692
1wy7 SAHUncharacterized protein / 0.691
2g1p SAHDNA adenine methylase 2.1.1.72 0.691
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.691
2xvm SAHTellurite methyltransferase 2.1.1.265 0.691
3wdm ADN4-phosphopantoate--beta-alanine ligase 6.3.2.36 0.691
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.691
4yac NAIC alpha-dehydrogenase / 0.691
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.691
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.690
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.690
2hnk SAHSAM-dependent O-methyltransferase / 0.690
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.690
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.690
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.689
2zfu SAHRibosomal RNA-processing protein 8 / 0.689
1uay ADNOxidoreductase / 0.688
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.688
4uy6 SAHHistidine N-alpha-methyltransferase / 0.688
1eg2 MTAModification methylase RsrI 2.1.1.72 0.687
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.687
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.687
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.687
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.687
2jae FADL-amino acid oxidase / 0.686
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.686
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.685
4qnu GEKtRNA U34 carboxymethyltransferase / 0.685
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.684
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.684
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.684
3tsc NADUncharacterized protein / 0.684
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.684
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.684
2i9k SAHModification methylase HhaI 2.1.1.37 0.683
2p5u NADUDP-glucose 4-epimerase / 0.683
3dh0 SAMUncharacterized protein / 0.683
3ldf SAHUncharacterized protein / 0.683
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.683
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.683
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.683
1fjx SAHModification methylase HhaI 2.1.1.37 0.681
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.681
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.681
2fkn NADUrocanate hydratase 4.2.1.49 0.681
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.681
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.681
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.681
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.681
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.681
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.680
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.680
3duw SAHO-methyltransferase, putative / 0.680
3p9k SAHCaffeic acid O-methyltransferase / 0.680
2o07 MTASpermidine synthase 2.5.1.16 0.679
4pgh SAMCaffeic acid O-methyltransferase / 0.679
4rtj SFGDNA adenine methylase 2.1.1.72 0.679
3fpf MTAUncharacterized protein / 0.678
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.678
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.678
1ptj SNDNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.677
2v7g NADUrocanate hydratase 4.2.1.49 0.677
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.676
4g67 SAHUncharacterized ACR, COG1565 superfamily / 0.676
4gc9 SAMDimethyladenosine transferase 1, mitochondrial 2.1.1 0.676
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.675
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.675
3lst SAHCalO1 / 0.675
4x3q SAHSibL / 0.675
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.674
4e2x SAHMethyltransferase / 0.674
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.673
3rfx NADUronate dehydrogenase / 0.673
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.673
5eku SAHArginine N-methyltransferase, putative / 0.673
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.672
3lhd SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.672
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.672
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.671
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.671
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.671
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.670
4dmg SAMUncharacterized protein / 0.670
4yv2 S4MSpermidine synthase, putative / 0.670
1skm SAHModification methylase HhaI 2.1.1.37 0.669
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.669
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.669
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.668
4dkj SAHCytosine-specific methyltransferase / 0.668
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.667
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.667
4mb2 ATPUncharacterized protein / 0.666
5epe SAHUncharacterized protein / 0.666
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.666
2z6u SAHModification methylase HhaI 2.1.1.37 0.664
4h0n SAHDnmt2 / 0.664
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.663
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.663
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.663
4c05 SAHProtein arginine N-methyltransferase 6 / 0.663
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.663
2cdu ADPNADH oxidase / 0.662
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.662
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.662
1af7 SAHChemotaxis protein methyltransferase 2.1.1.80 0.661
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.661
3bus SAHDemethylrebeccamycin-D-glucose O-methyltransferase / 0.661
3c3y SAHO-methyltransferase / 0.661
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.661
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.661
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.660
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.659
3fri SAH16S rRNA methylase / 0.659
1mht SAHModification methylase HhaI 2.1.1.37 0.658
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.658
4d79 ATPtRNA threonylcarbamoyladenosine dehydratase 6.1 0.658
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.656
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.656
3bwc SAMSpermidine synthase, putative / 0.656
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.655
3p9c SAHCaffeic acid O-methyltransferase / 0.655
3tr6 SAHO-methyltransferase / 0.655
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.655
1n4w FADCholesterol oxidase 1.1.3.6 0.654
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.654
4xxg FADCholesterol oxidase 1.1.3.6 0.654
7mht SAHModification methylase HhaI 2.1.1.37 0.654
1b4v FADCholesterol oxidase 1.1.3.6 0.653
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.653
2c7q SAHModification methylase HhaI 2.1.1.37 0.653
4tm3 FADKtzI / 0.653
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.650
4fn4 NADShort chain dehydrogenase / 0.650