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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
3sxj SAM Putative methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3sxj SAMPutative methyltransferase / 1.004
3t0i SAHPutative methyltransferase / 0.954
3t7s SAMUncharacterized protein / 0.925
3kkz SAMUncharacterized protein / 0.858
3t7t SAHUncharacterized protein / 0.812
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.749
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.741
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.740
3p9k SAHCaffeic acid O-methyltransferase / 0.739
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.736
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.727
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.722
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.717
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.713
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.711
2yqz SAMUncharacterized protein / 0.710
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.707
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.706
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.704
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.704
3e23 SAMUncharacterized protein / 0.703
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.701
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.699
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.698
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.697
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.696
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.696
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.694
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.694
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.693
4nec SAHPutative SAM-dependent methyltransferase / 0.693
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.692
3fri SAH16S rRNA methylase / 0.691
4uy6 SAHHistidine N-alpha-methyltransferase / 0.689
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.688
3h03 UBPGlutamate receptor 2 / 0.687
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.686
3e8s SAHUncharacterized protein / 0.685
3zzh NLGProtein ARG5,6, mitochondrial 2.7.2.8 0.684
3c36 KAIGlutamate receptor ionotropic, kainate 1 / 0.683
5bp9 SAHPutative methyltransferase protein / 0.682
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.680
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.678
3lcc SAHThiocyanate methyltransferase 1 / 0.678
5epe SAHUncharacterized protein / 0.678
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.677
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.676
2rd5 NLGAcetylglutamate kinase, chloroplastic 2.7.2.8 0.676
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.676
3c34 KAIGlutamate receptor ionotropic, kainate 1 / 0.674
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.673
4hh4 SAHCcbJ / 0.673
2qs1 UB1Glutamate receptor ionotropic, kainate 1 / 0.670
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.669
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.669
3s2v 3HUGlutamate receptor ionotropic, kainate 1 / 0.669
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.668
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.668
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.668
4ie0 PD2Alpha-ketoglutarate-dependent dioxygenase FTO / 0.668
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.667
2tpl HPPTyrosine phenol-lyase 4.1.99.2 0.667
2xvm SAHTellurite methyltransferase 2.1.1.265 0.667
4kvz SAHPtnL protein / 0.667
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.666
4dld TZGGlutamate receptor ionotropic, kainate 1 / 0.665
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.664
1ve3 SAMUncharacterized protein / 0.664
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.663
5jdz SAHMethyl transferase / 0.663
1vso AT1Glutamate receptor ionotropic, kainate 1 / 0.661
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.661
2wba NDPTrypanothione reductase 1.8.1.12 0.660
3lst SAHCalO1 / 0.658
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.658
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.657
3ua3 SAHProtein arginine N-methyltransferase 5 / 0.654
4g67 SAHUncharacterized ACR, COG1565 superfamily / 0.654
1dhf FOLDihydrofolate reductase 1.5.1.3 0.653
3sx2 NADUncharacterized protein / 0.652
4pne SAHMethyltransferase-like protein / 0.652
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.651
2qs3 UBEGlutamate receptor ionotropic, kainate 1 / 0.650
4kwc SAHMethyltransferase domain family / 0.650
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.650