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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
1y9d FAD Pyruvate oxidase 1.2.3.3

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1y9d FADPyruvate oxidase 1.2.3.3 0.930
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.741
1pow FADPyruvate oxidase 1.2.3.3 0.736
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.735
3lcc SAHThiocyanate methyltransferase 1 / 0.732
1v5e FADPyruvate oxidase / 0.731
4nec SAHPutative SAM-dependent methyltransferase / 0.728
3ldf SAHUncharacterized protein / 0.725
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.723
3go4 SAHUncharacterized protein / 0.720
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.712
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.710
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.710
2g1p SAHDNA adenine methylase 2.1.1.72 0.709
2o07 MTASpermidine synthase 2.5.1.16 0.709
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.708
3bwc SAMSpermidine synthase, putative / 0.708
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.708
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.707
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.705
3kkz SAMUncharacterized protein / 0.703
2ibt NEAModification methylase TaqI 2.1.1.72 0.701
4dmg SAMUncharacterized protein / 0.701
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.700
2o06 MTASpermidine synthase 2.5.1.16 0.700
3ea4 FABAcetolactate synthase, chloroplastic 2.2.1.6 0.698
4kvz SAHPtnL protein / 0.698
2dji FADPyruvate oxidase / 0.697
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.697
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.696
2np7 NEAModification methylase TaqI 2.1.1.72 0.696
3ou6 SAMSAM-dependent methyltransferase / 0.696
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.696
4yv2 S4MSpermidine synthase, putative / 0.696
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.694
2qe6 SAMUncharacterized protein / 0.694
2pan FADGlyoxylate carboligase 4.1.1.47 0.693
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.692
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.691
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.689
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.688
5je2 SAHMethyl transferase / 0.687
1boo SAHModification methylase PvuII 2.1.1.113 0.686
4yuv S4MSpermidine synthase, putative / 0.686
4yuz S4MSpermidine synthase, putative / 0.686
2pt6 S4MSpermidine synthase / 0.685
1wy7 SAHUncharacterized protein / 0.684
3c3y SAHO-methyltransferase / 0.684
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.683
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.682
3mht SAHModification methylase HhaI 2.1.1.37 0.680
5je4 SAHMethyl transferase / 0.680
1g1a NADdTDP-glucose 4,6-dehydratase / 0.679
5je3 SAHMethyl transferase / 0.679
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.679
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.678
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.678
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.678
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.678
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.678
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.678
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.678
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.677
4yv0 S4MSpermidine synthase, putative / 0.677
5ahk FADAcetolactate synthase II, large subunit / 0.677
2i9k SAHModification methylase HhaI 2.1.1.37 0.676
3clu FADElectron transfer flavoprotein subunit alpha / 0.676
3mj4 FADUDP-galactopyranose mutase / 0.676
5jdz SAHMethyl transferase / 0.676
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.675
2yxl SFG450aa long hypothetical fmu protein / 0.675
2b4y APRNAD-dependent protein deacylase sirtuin-5, mitochondrial / 0.673
3s55 NADPutative short-chain dehydrogenase/reductase / 0.673
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.673
2gs9 SAHUncharacterized protein / 0.672
4yac NAIC alpha-dehydrogenase / 0.672
1skm SAHModification methylase HhaI 2.1.1.37 0.671
3ou7 SAMSAM-dependent methyltransferase / 0.671
4eki 0QKHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.671
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.670
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.670
4yv1 S4MSpermidine synthase, putative / 0.670
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.669
4fn4 NADShort chain dehydrogenase / 0.669
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.668
3clr FADElectron transfer flavoprotein subunit alpha / 0.667
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.666
3p9c SAHCaffeic acid O-methyltransferase / 0.666
5f8f SFGPossible transcriptional regulatory protein / 0.666
1g60 SAMModification methylase MboII 2.1.1.72 0.665
3fpf MTAUncharacterized protein / 0.665
7mht SAHModification methylase HhaI 2.1.1.37 0.665
2yg4 FADPutrescine oxidase / 0.664
2fkn NADUrocanate hydratase 4.2.1.49 0.662
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.661
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.660
3t7s SAMUncharacterized protein / 0.660
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.660
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.659
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.657
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.657
4x3q SAHSibL / 0.657
5bxy SAHPutative RNA methylase family UPF0020 / 0.657
5i39 FADL-amino acid deaminase / 0.657
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.656
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.656
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.656
2hmv ADPKtr system potassium uptake protein A / 0.655
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.654
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.654
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.653
4kwc SAHMethyltransferase domain family / 0.653
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.652
3p9k SAHCaffeic acid O-methyltransferase / 0.652
4gdp FADPolyamine oxidase FMS1 / 0.652
4poo SAMPutative RNA methylase / 0.652
4d5g FADCyclohexane-1,2-dione hydrolase 3.7.1.11 0.650
4eqg A5AHistidine triad nucleotide-binding protein 1 3 0.650
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.650
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.650