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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
2p35 SAH Trans-aconitate 2-methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
2p35 SAHTrans-aconitate 2-methyltransferase / 0.917
2yqz SAMUncharacterized protein / 0.798
5je4 SAHMethyl transferase / 0.787
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.769
5je3 SAHMethyl transferase / 0.767
5jdz SAHMethyl transferase / 0.764
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.763
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.762
5je2 SAHMethyl transferase / 0.761
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.760
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.755
3lcc SAHThiocyanate methyltransferase 1 / 0.755
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.750
4lwp SAHArginine N-methyltransferase, putative / 0.750
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.742
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.741
4kwc SAHMethyltransferase domain family / 0.740
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.736
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.736
2qe6 SAMUncharacterized protein / 0.734
2c7q SAHModification methylase HhaI 2.1.1.37 0.733
4c04 SFGProtein arginine N-methyltransferase 6 / 0.733
3fri SAH16S rRNA methylase / 0.732
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.731
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.731
3go4 SAHUncharacterized protein / 0.730
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.729
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.727
4qpp SAHProtein arginine N-methyltransferase 6 / 0.727
5bxy SAHPutative RNA methylase family UPF0020 / 0.727
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.726
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.726
2gs9 SAHUncharacterized protein / 0.725
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.725
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.725
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.725
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.725
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.724
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.724
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.722
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.720
5epe SAHUncharacterized protein / 0.720
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.719
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.719
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.717
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.715
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.714
4nec SAHPutative SAM-dependent methyltransferase / 0.714
3t7s SAMUncharacterized protein / 0.713
5bp9 SAHPutative methyltransferase protein / 0.713
2zfu SAHRibosomal RNA-processing protein 8 / 0.711
3bus SAHDemethylrebeccamycin-D-glucose O-methyltransferase / 0.711
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.711
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.710
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.710
5bp7 SAHSAM-dependent methyltransferase / 0.710
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.709
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.709
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.708
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.707
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.707
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.705
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.704
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.704
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.703
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.703
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.702
7mht SAHModification methylase HhaI 2.1.1.37 0.701
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.700
3kkz SAMUncharacterized protein / 0.698
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.698
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.698
1orh SAHProtein arginine N-methyltransferase 1 / 0.697
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.697
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.697
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.697
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.696
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.696
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.695
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.695
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.695
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.694
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.693
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.693
4hh4 SAHCcbJ / 0.693
4yuz S4MSpermidine synthase, putative / 0.693
3cbg SAHO-methyltransferase / 0.692
4uy6 SAHHistidine N-alpha-methyltransferase / 0.692
3bwc SAMSpermidine synthase, putative / 0.691
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.690
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.690
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.690
3icp NADNAD-dependent epimerase/dehydratase / 0.689
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.689
3p9k SAHCaffeic acid O-methyltransferase / 0.688
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.688
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.686
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.686
3wds NADNADH-dependent quinuclidinone reductase / 0.686
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.685
1ori SAHProtein arginine N-methyltransferase 1 / 0.684
4yac NAIC alpha-dehydrogenase / 0.684
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.683
3c3y SAHO-methyltransferase / 0.683
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.683
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.682
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.682
3gu3 SAHMethyltransferase / 0.682
3hvk 719Catechol O-methyltransferase 2.1.1.6 0.682
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.681
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.681
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.681
1af7 SAHChemotaxis protein methyltransferase 2.1.1.80 0.680
1orr NADCDP-paratose 2-epimerase / 0.680
2hms NAIKtr system potassium uptake protein A / 0.680
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.680
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.680
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.680
3lst SAHCalO1 / 0.680
4c03 SFGProtein arginine N-methyltransferase 6 / 0.680
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.679
4rvd SAMD-mycarose 3-C-methyltransferase / 0.679
4wec NADShort chain dehydrogenase / 0.679
4e2x SAHMethyltransferase / 0.678
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.678
2uyh SAHModification methylase HhaI 2.1.1.37 0.677
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.677
4pgh SAMCaffeic acid O-methyltransferase / 0.677
5f8f SFGPossible transcriptional regulatory protein / 0.677
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.676
2ewm NAD(S)-1-Phenylethanol dehydrogenase 1.1.1.311 0.676
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.676
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.676
9mht SAHModification methylase HhaI 2.1.1.37 0.676
3duw SAHO-methyltransferase, putative / 0.675
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.675
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.674
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.673
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.673
3ou6 SAMSAM-dependent methyltransferase / 0.673
3t7t SAHUncharacterized protein / 0.673
3tm4 SAMUncharacterized protein / 0.673
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.672
3dh0 SAMUncharacterized protein / 0.672
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.672
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.671
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.671
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.671
3mht SAHModification methylase HhaI 2.1.1.37 0.671
4yai NAIC alpha-dehydrogenase / 0.671
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.670
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.669
2fkn NADUrocanate hydratase 4.2.1.49 0.669
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.669
2yxl SFG450aa long hypothetical fmu protein / 0.669
3e8s SAHUncharacterized protein / 0.669
3e23 SAMUncharacterized protein / 0.668
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.668
1skm SAHModification methylase HhaI 2.1.1.37 0.667
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.667
4kvz SAHPtnL protein / 0.667
4qnv GEKtRNA U34 carboxymethyltransferase / 0.667
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.667
1pow FADPyruvate oxidase 1.2.3.3 0.666
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.666
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.666
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.666
5jla NADPutative short-chain dehydrogenase/reductase / 0.666
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.665
3p2k SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.665
4fn4 NADShort chain dehydrogenase / 0.665
4rtk SAHDNA adenine methylase 2.1.1.72 0.665
4yag NAIC alpha-dehydrogenase / 0.665
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.664
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.664
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.664
2np7 NEAModification methylase TaqI 2.1.1.72 0.663
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.663
3ou7 SAMSAM-dependent methyltransferase / 0.663
4gbe SAHDNA adenine methylase 2.1.1.72 0.663
1g1a NADdTDP-glucose 4,6-dehydratase / 0.662
2cdu ADPNADH oxidase / 0.662
3ea4 FABAcetolactate synthase, chloroplastic 2.2.1.6 0.662
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.662
4nzh FADL-ornithine N(5)-monooxygenase / 0.662
4yv2 S4MSpermidine synthase, putative / 0.662
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.661
2c20 NADUDP-glucose 4-epimerase / 0.661
2hmv ADPKtr system potassium uptake protein A / 0.661
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.661
4id9 NADPutative UDP-glucose 4-epimerase / 0.661
2e1m FADL-glutamate oxidase / 0.660
2np6 NEAModification methylase TaqI 2.1.1.72 0.660
2xvm SAHTellurite methyltransferase 2.1.1.265 0.660
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.660
3ldf SAHUncharacterized protein / 0.660
4tlz FADKtzI / 0.660
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.659
1hzz NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.659
1n4v FADCholesterol oxidase 1.1.3.6 0.659
4xxg FADCholesterol oxidase 1.1.3.6 0.659
2c59 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.658
2gew FADCholesterol oxidase 1.1.3.6 0.658
2oy0 SAHGenome polyprotein / 0.658
3fpf MTAUncharacterized protein / 0.658
3tm5 SFGUncharacterized protein / 0.658
3tos SAHCalS11 / 0.658
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.657
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.657
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.657
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.655
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.655
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.655
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.655
3n1s 5GPPurine nucleoside phosphoramidase / 0.655
4egu 5GPPutative histidine triad (HIT) protein / 0.655
5mht SAHModification methylase HhaI 2.1.1.37 0.655
1uay ADNOxidoreductase / 0.654
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.654
2p5y NADUDP-glucose 4-epimerase / 0.654
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.654
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.654
3b6d FAECholesterol oxidase 1.1.3.6 0.654
3cox FADCholesterol oxidase 1.1.3.6 0.653
4eqg A5AHistidine triad nucleotide-binding protein 1 3 0.653
4qi4 FADCellobiose dehydrogenase / 0.653
4tm4 FDAKtzI / 0.653
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.653
1wy7 SAHUncharacterized protein / 0.652
2i9k SAHModification methylase HhaI 2.1.1.37 0.652
4c05 SAHProtein arginine N-methyltransferase 6 / 0.652
4eqe KAAHistidine triad nucleotide-binding protein 1 3 0.652
1f3l SAHProtein arginine N-methyltransferase 3 / 0.651
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.651
2pxa SAHGenome polyprotein 2.7.7.48 0.651
1e6e FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.650
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.650
2fk8 SAMHydroxymycolate synthase MmaA4 2.1.1 0.650
2p5u NADUDP-glucose 4-epimerase / 0.650
2z6u SAHModification methylase HhaI 2.1.1.37 0.650
3ha5 SFGHydroxymycolate synthase MmaA4 2.1.1 0.650