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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
3pb3 SAH 16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.934
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.888
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.754
4nec SAHPutative SAM-dependent methyltransferase / 0.736
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.728
5je2 SAHMethyl transferase / 0.728
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.722
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.722
4kvz SAHPtnL protein / 0.722
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.718
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.709
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.709
1f3l SAHProtein arginine N-methyltransferase 3 / 0.706
2qe6 SAMUncharacterized protein / 0.705
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.705
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.704
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.703
3kkz SAMUncharacterized protein / 0.703
3go4 SAHUncharacterized protein / 0.702
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.699
2yqz SAMUncharacterized protein / 0.698
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.697
1ve3 SAMUncharacterized protein / 0.696
2p35 SAHTrans-aconitate 2-methyltransferase / 0.695
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.694
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.691
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.690
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.690
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.688
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.687
3lst SAHCalO1 / 0.687
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.685
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.684
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.683
3p9k SAHCaffeic acid O-methyltransferase / 0.683
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.683
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.682
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.682
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.681
4kwc SAHMethyltransferase domain family / 0.681
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.680
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.678
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.675
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.674
1uay ADNOxidoreductase / 0.673
4hh4 SAHCcbJ / 0.673
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.672
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.671
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.671
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.670
3fpf MTAUncharacterized protein / 0.670
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.669
3t7s SAMUncharacterized protein / 0.669
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.668
4c03 SFGProtein arginine N-methyltransferase 6 / 0.668
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.667
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.667
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.667
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.666
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.666
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.665
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.665
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.665
2zfu SAHRibosomal RNA-processing protein 8 / 0.664
2zif SAMMethyltransferase / 0.663
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.663
4qpp SAHProtein arginine N-methyltransferase 6 / 0.662
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.661
3mht SAHModification methylase HhaI 2.1.1.37 0.660
5bxy SAHPutative RNA methylase family UPF0020 / 0.660
1skm SAHModification methylase HhaI 2.1.1.37 0.659
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.659
4yac NAIC alpha-dehydrogenase / 0.659
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.658
5bp7 SAHSAM-dependent methyltransferase / 0.658
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.657
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.657
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.656
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.656
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.653
3t7t SAHUncharacterized protein / 0.653
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.652
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.652
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.652
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.652
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.652
1vq1 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.651
2pt6 S4MSpermidine synthase / 0.651
3e8s SAHUncharacterized protein / 0.651
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.651
4qnu GEKtRNA U34 carboxymethyltransferase / 0.651
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.650
3gu3 SAHMethyltransferase / 0.650
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.650