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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
1wy7 SAH Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1wy7 SAHUncharacterized protein / 0.929
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.739
3s55 NADPutative short-chain dehydrogenase/reductase / 0.728
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.715
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.715
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.713
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.710
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.708
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.705
5je2 SAHMethyl transferase / 0.705
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.702
3sx2 NADUncharacterized protein / 0.702
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.702
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.701
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.701
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.701
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.700
3e23 SAMUncharacterized protein / 0.699
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.699
2qe6 SAMUncharacterized protein / 0.698
2yqz SAMUncharacterized protein / 0.696
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.695
4yac NAIC alpha-dehydrogenase / 0.695
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.694
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.694
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.694
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.694
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.693
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.692
4c03 SFGProtein arginine N-methyltransferase 6 / 0.692
3go4 SAHUncharacterized protein / 0.691
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.691
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.691
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.691
5epe SAHUncharacterized protein / 0.691
1orr NADCDP-paratose 2-epimerase / 0.690
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.690
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.690
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.689
3kkz SAMUncharacterized protein / 0.689
4uy6 SAHHistidine N-alpha-methyltransferase / 0.688
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.687
3hvi 619Catechol O-methyltransferase 2.1.1.6 0.687
1g60 SAMModification methylase MboII 2.1.1.72 0.686
3lby SAHUncharacterized protein / 0.686
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.685
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.685
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.685
4yuz S4MSpermidine synthase, putative / 0.685
1y9d FADPyruvate oxidase 1.2.3.3 0.684
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.684
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.684
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.683
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.683
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.682
4yv0 S4MSpermidine synthase, putative / 0.682
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.682
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.681
3ea4 FABAcetolactate synthase, chloroplastic 2.2.1.6 0.680
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.680
5bxy SAHPutative RNA methylase family UPF0020 / 0.680
5f8f SFGPossible transcriptional regulatory protein / 0.680
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.679
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.679
2pan FADGlyoxylate carboligase 4.1.1.47 0.678
3bwc SAMSpermidine synthase, putative / 0.678
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.678
4kvz SAHPtnL protein / 0.678
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.677
3e8s SAHUncharacterized protein / 0.677
3e9y FABAcetolactate synthase, chloroplastic 2.2.1.6 0.677
4wec NADShort chain dehydrogenase / 0.677
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.676
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.675
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.675
2o07 MTASpermidine synthase 2.5.1.16 0.674
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.674
1jnz FADAdenylylsulfate reductase, subunit A (AprA) / 0.673
3ldg SAHUncharacterized protein / 0.673
4poo SAMPutative RNA methylase / 0.673
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.672
4kwc SAHMethyltransferase domain family / 0.672
3duw SAHO-methyltransferase, putative / 0.671
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.671
4gll NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.671
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.670
2yy7 NADL-threonine dehydrogenase / 0.670
3hvk 719Catechol O-methyltransferase 2.1.1.6 0.670
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.670
4lis NADUDP-glucose 4-epimerase (Eurofung) / 0.670
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.669
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.669
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.669
1eg2 MTAModification methylase RsrI 2.1.1.72 0.668
3g5s FADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / 0.668
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.667
2cvj FADThioredoxin reductase related protein / 0.667
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.667
2o06 MTASpermidine synthase 2.5.1.16 0.666
3c3y SAHO-methyltransferase / 0.666
3geg NADShort-chain dehydrogenase/reductase SDR / 0.666
4yuv S4MSpermidine synthase, putative / 0.666
5f2k SAHUncharacterized protein / 0.666
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.665
3fri SAH16S rRNA methylase / 0.665
3lhd SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.665
1boo SAHModification methylase PvuII 2.1.1.113 0.664
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.664
4lwp SAHArginine N-methyltransferase, putative / 0.664
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.663
2f8l SAMLmo1582 protein / 0.663
3eey SAMrRNA methylase / 0.663
3rw9 DSHSpermidine synthase 2.5.1.16 0.663
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.663
4e2x SAHMethyltransferase / 0.663
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.663
4m55 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.663
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.663
5jla NADPutative short-chain dehydrogenase/reductase / 0.663
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.662
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.662
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.662
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.662
4x3q SAHSibL / 0.662
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.662
1ve3 SAMUncharacterized protein / 0.661
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.661
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.661
5eku SAHArginine N-methyltransferase, putative / 0.661
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.660
1nw5 SAMModification methylase RsrI 2.1.1.72 0.659
2np6 NEAModification methylase TaqI 2.1.1.72 0.659
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.659
3ak4 NADNADH-dependent quinuclidinone reductase / 0.659
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.658
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.658
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.658
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.657
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.656
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.656
1skm SAHModification methylase HhaI 2.1.1.37 0.655
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.655
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.655
3lcc SAHThiocyanate methyltransferase 1 / 0.655
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.655
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.655
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.655
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.654
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.654
4egb NADdTDP-glucose 4,6-dehydratase / 0.654
1f3l SAHProtein arginine N-methyltransferase 3 / 0.653
1nw6 SFGModification methylase RsrI 2.1.1.72 0.653
2ylx FADPhenylacetone monooxygenase 1.14.13.92 0.653
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.653
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.653
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.653
4ctj SAMGenome polyprotein / 0.653
4fr0 SAMArsenic methyltransferase / 0.653
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.652
2p35 SAHTrans-aconitate 2-methyltransferase / 0.652
3iv6 SAMUncharacterized protein / 0.652
3lkz SFGGenome polyprotein / 0.652
3t7s SAMUncharacterized protein / 0.652
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.652
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.651
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.651
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.651
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.651
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.650
2fkn NADUrocanate hydratase 4.2.1.49 0.650
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.650
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.650