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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
3p9c SAH Caffeic acid O-methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3p9c SAHCaffeic acid O-methyltransferase / 0.884
4pgh SAMCaffeic acid O-methyltransferase / 0.788
3p9k SAHCaffeic acid O-methyltransferase / 0.767
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.723
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.721
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.716
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.712
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.712
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.710
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.704
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.696
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.691
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.691
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.691
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.690
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.689
3fri SAH16S rRNA methylase / 0.689
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.689
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.685
3kkz SAMUncharacterized protein / 0.685
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.685
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.685
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.684
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.683
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.682
1x1c SAHC-20 methyltransferase / 0.682
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.682
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.682
2yqz SAMUncharacterized protein / 0.681
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.680
3lst SAHCalO1 / 0.680
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.680
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.679
3ou2 SAHSAM-dependent methyltransferase / 0.678
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.677
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.677
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.675
5bp9 SAHPutative methyltransferase protein / 0.674
2qe6 SAMUncharacterized protein / 0.673
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.673
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.672
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.667
1uay ADNOxidoreductase / 0.666
1y9d FADPyruvate oxidase 1.2.3.3 0.666
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.666
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.666
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.664
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.663
4nec SAHPutative SAM-dependent methyltransferase / 0.663
5bxy SAHPutative RNA methylase family UPF0020 / 0.660
5je4 SAHMethyl transferase / 0.660
1f3l SAHProtein arginine N-methyltransferase 3 / 0.659
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.658
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.658
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.656
5jdz SAHMethyl transferase / 0.656
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.655
3bwc SAMSpermidine synthase, putative / 0.655
3go4 SAHUncharacterized protein / 0.655
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.654
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.654
4yv0 S4MSpermidine synthase, putative / 0.654
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.653
5je2 SAHMethyl transferase / 0.653
1pow FADPyruvate oxidase 1.2.3.3 0.652
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.652
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.652
4kwc SAHMethyltransferase domain family / 0.652
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.651
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.651
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.651
4yv1 S4MSpermidine synthase, putative / 0.651
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.650