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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
2qe6 SAM Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2qe6 SAMUncharacterized protein / 1.085
3go4 SAHUncharacterized protein / 0.850
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.812
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.800
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.796
3lcc SAHThiocyanate methyltransferase 1 / 0.786
5jdz SAHMethyl transferase / 0.784
5je3 SAHMethyl transferase / 0.784
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.782
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.779
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.771
4nec SAHPutative SAM-dependent methyltransferase / 0.765
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.762
1f3l SAHProtein arginine N-methyltransferase 3 / 0.760
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.760
5je4 SAHMethyl transferase / 0.759
3kkz SAMUncharacterized protein / 0.756
5bp7 SAHSAM-dependent methyltransferase / 0.755
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.753
2gs9 SAHUncharacterized protein / 0.752
3mht SAHModification methylase HhaI 2.1.1.37 0.752
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.752
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.752
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.751
3ou2 SAHSAM-dependent methyltransferase / 0.751
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.750
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.749
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.748
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.748
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.746
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.743
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.743
3e8s SAHUncharacterized protein / 0.743
2yqz SAMUncharacterized protein / 0.742
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.742
4e2x SAHMethyltransferase / 0.742
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.740
5epe SAHUncharacterized protein / 0.736
3t7s SAMUncharacterized protein / 0.735
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.735
2p35 SAHTrans-aconitate 2-methyltransferase / 0.734
2i9k SAHModification methylase HhaI 2.1.1.37 0.732
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.732
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.732
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.731
4qpp SAHProtein arginine N-methyltransferase 6 / 0.731
3ou6 SAMSAM-dependent methyltransferase / 0.730
3fri SAH16S rRNA methylase / 0.729
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.726
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.726
4x3q SAHSibL / 0.725
4uy6 SAHHistidine N-alpha-methyltransferase / 0.722
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.722
5je2 SAHMethyl transferase / 0.722
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.719
5bp9 SAHPutative methyltransferase protein / 0.719
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.718
4fr0 SAMArsenic methyltransferase / 0.718
4qnv GEKtRNA U34 carboxymethyltransferase / 0.717
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.716
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.716
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.716
4qnu GEKtRNA U34 carboxymethyltransferase / 0.716
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.715
4c04 SFGProtein arginine N-methyltransferase 6 / 0.714
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.712
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.712
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.712
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.711
5bxy SAHPutative RNA methylase family UPF0020 / 0.710
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.709
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.705
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.705
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.705
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.705
4hh4 SAHCcbJ / 0.705
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.703
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.702
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.702
4pne SAHMethyltransferase-like protein / 0.701
1ve3 SAMUncharacterized protein / 0.700
2fkn NADUrocanate hydratase 4.2.1.49 0.700
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.699
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.699
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.699
1wy7 SAHUncharacterized protein / 0.698
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.698
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.696
3t7t SAHUncharacterized protein / 0.696
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.695
5f8f SFGPossible transcriptional regulatory protein / 0.695
1y9d FADPyruvate oxidase 1.2.3.3 0.694
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.694
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.693
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.693
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.693
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.693
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.693
2o06 MTASpermidine synthase 2.5.1.16 0.692
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.691
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.691
4c03 SFGProtein arginine N-methyltransferase 6 / 0.691
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.689
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.688
3duw SAHO-methyltransferase, putative / 0.688
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.687
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.687
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.686
1ori SAHProtein arginine N-methyltransferase 1 / 0.685
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.685
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.685
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.684
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.684
2hms NAIKtr system potassium uptake protein A / 0.683
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.682
4yac NAIC alpha-dehydrogenase / 0.682
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.682
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.682
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.681
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.681
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.681
4mb2 ATPUncharacterized protein / 0.681
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.680
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.679
3lst SAHCalO1 / 0.679
4kwc SAHMethyltransferase domain family / 0.679
5eku SAHArginine N-methyltransferase, putative / 0.679
3c3y SAHO-methyltransferase / 0.678
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.677
2zfu SAHRibosomal RNA-processing protein 8 / 0.676
3p9k SAHCaffeic acid O-methyltransferase / 0.676
4lwp SAHArginine N-methyltransferase, putative / 0.676
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.675
3fpf MTAUncharacterized protein / 0.675
10mh SAHModification methylase HhaI 2.1.1.37 0.674
2ewm NAD(S)-1-Phenylethanol dehydrogenase 1.1.1.311 0.674
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.674
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.673
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.673
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.673
3p9c SAHCaffeic acid O-methyltransferase / 0.673
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.672
2v7g NADUrocanate hydratase 4.2.1.49 0.672
3mj4 FADUDP-galactopyranose mutase / 0.672
4dkj SAHCytosine-specific methyltransferase / 0.672
4yv1 S4MSpermidine synthase, putative / 0.671
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.671
4rvd SAMD-mycarose 3-C-methyltransferase / 0.670
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.669
2br5 SAHCephalosporin hydroxylase CmcI / 0.669
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.669
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.669
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.669
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.668
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.667
4c05 SAHProtein arginine N-methyltransferase 6 / 0.667
2o07 MTASpermidine synthase 2.5.1.16 0.666
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.666
3wds NADNADH-dependent quinuclidinone reductase / 0.666
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.665
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.665
4oa5 SAHO-methyltransferase family protein / 0.664
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.664
1mht SAHModification methylase HhaI 2.1.1.37 0.663
1x1c SAHC-20 methyltransferase / 0.663
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.662
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.661
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.661
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.661
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.661
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.661
4eqg A5AHistidine triad nucleotide-binding protein 1 3 0.661
4pgh SAMCaffeic acid O-methyltransferase / 0.661
3rfx NADUronate dehydrogenase / 0.660
3wv7 ADPHmd co-occurring protein HcgE / 0.660
4gbe SAHDNA adenine methylase 2.1.1.72 0.660
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.659
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.659
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.659
2dki FAD3-hydroxybenzoate 4-monooxygenase 1.14.13.23 0.658
2oy0 SAHGenome polyprotein / 0.657
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.657
1hzz NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.656
1yf3 SAHDNA adenine methylase / 0.656
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.656
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.656
2hmv ADPKtr system potassium uptake protein A / 0.654
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.654
1skm SAHModification methylase HhaI 2.1.1.37 0.653
1uay ADNOxidoreductase / 0.653
3t0i SAHPutative methyltransferase / 0.653
2c7q SAHModification methylase HhaI 2.1.1.37 0.652
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.651
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.650
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.650
4d79 ATPtRNA threonylcarbamoyladenosine dehydratase 6.1 0.650