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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
4a6d SAM Acetylserotonin O-methyltransferase 2.1.1.4

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 1.096
3p9k SAHCaffeic acid O-methyltransferase / 0.825
3e8s SAHUncharacterized protein / 0.815
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.807
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.800
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.774
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.768
3fri SAH16S rRNA methylase / 0.757
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.754
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.750
4x3q SAHSibL / 0.749
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.735
3lst SAHCalO1 / 0.731
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.730
3kkz SAMUncharacterized protein / 0.729
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.729
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.729
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.728
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.726
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.726
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.718
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.717
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.717
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.714
2gs9 SAHUncharacterized protein / 0.711
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.709
2qe6 SAMUncharacterized protein / 0.705
4kwc SAHMethyltransferase domain family / 0.705
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.703
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.703
2yqz SAMUncharacterized protein / 0.702
3gu3 SAHMethyltransferase / 0.702
4hh4 SAHCcbJ / 0.701
4uy6 SAHHistidine N-alpha-methyltransferase / 0.701
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.700
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.699
3t7s SAMUncharacterized protein / 0.699
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.698
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.697
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.697
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.696
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.691
5bp9 SAHPutative methyltransferase protein / 0.691
3e23 SAMUncharacterized protein / 0.689
4e2x SAHMethyltransferase / 0.688
4nec SAHPutative SAM-dependent methyltransferase / 0.688
2xvm SAHTellurite methyltransferase 2.1.1.265 0.686
3go4 SAHUncharacterized protein / 0.684
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.684
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.684
5f8f SFGPossible transcriptional regulatory protein / 0.684
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.683
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.681
3t0i SAHPutative methyltransferase / 0.680
3p9c SAHCaffeic acid O-methyltransferase / 0.677
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.677
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.675
4c03 SFGProtein arginine N-methyltransferase 6 / 0.675
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.674
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.674
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.672
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.671
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.669
4kvz SAHPtnL protein / 0.669
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.668
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.666
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.666
3sxj SAMPutative methyltransferase / 0.666
5epe SAHUncharacterized protein / 0.664
1wy7 SAHUncharacterized protein / 0.663
3t7t SAHUncharacterized protein / 0.663
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.663
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.662
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.661
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.659
4pgh SAMCaffeic acid O-methyltransferase / 0.659
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.658
3ua3 SAHProtein arginine N-methyltransferase 5 / 0.658
1yf3 SAHDNA adenine methylase / 0.657
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.656
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.656
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.654
4c04 SFGProtein arginine N-methyltransferase 6 / 0.654
5jdz SAHMethyl transferase / 0.653
5je2 SAHMethyl transferase / 0.653
5je3 SAHMethyl transferase / 0.652
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.650