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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
2xvm SAH Tellurite methyltransferase 2.1.1.265

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2xvm SAHTellurite methyltransferase 2.1.1.265 1.041
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.787
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.786
1ve3 SAMUncharacterized protein / 0.765
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.763
3p9k SAHCaffeic acid O-methyltransferase / 0.758
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.756
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.756
3t7s SAMUncharacterized protein / 0.751
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.750
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.750
5je3 SAHMethyl transferase / 0.750
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.747
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.744
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.743
5jdz SAHMethyl transferase / 0.743
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.742
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.741
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.738
5je4 SAHMethyl transferase / 0.736
3e8s SAHUncharacterized protein / 0.735
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.732
4c03 SFGProtein arginine N-methyltransferase 6 / 0.732
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.729
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.721
3ou2 SAHSAM-dependent methyltransferase / 0.711
3t7t SAHUncharacterized protein / 0.711
1f3l SAHProtein arginine N-methyltransferase 3 / 0.709
4lwp SAHArginine N-methyltransferase, putative / 0.709
4nec SAHPutative SAM-dependent methyltransferase / 0.709
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.707
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.707
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.706
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.706
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.706
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.705
3lcc SAHThiocyanate methyltransferase 1 / 0.705
3lst SAHCalO1 / 0.704
3t0i SAHPutative methyltransferase / 0.704
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.703
1ori SAHProtein arginine N-methyltransferase 1 / 0.702
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.702
2zfu SAHRibosomal RNA-processing protein 8 / 0.702
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.702
4c04 SFGProtein arginine N-methyltransferase 6 / 0.701
4qpp SAHProtein arginine N-methyltransferase 6 / 0.701
4x3q SAHSibL / 0.701
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.697
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.696
4kvz SAHPtnL protein / 0.695
3fri SAH16S rRNA methylase / 0.694
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.692
3go4 SAHUncharacterized protein / 0.691
2yqz SAMUncharacterized protein / 0.686
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.686
4pgh SAMCaffeic acid O-methyltransferase / 0.686
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.685
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.685
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.685
1orh SAHProtein arginine N-methyltransferase 1 / 0.679
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.679
4kwc SAHMethyltransferase domain family / 0.679
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.678
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.677
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.675
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.674
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.673
3ha5 SFGHydroxymycolate synthase MmaA4 2.1.1 0.673
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.670
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.669
2fk8 SAMHydroxymycolate synthase MmaA4 2.1.1 0.669
3gu3 SAHMethyltransferase / 0.669
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.668
3sxj SAMPutative methyltransferase / 0.667
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.667
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.666
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.665
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.665
3kkz SAMUncharacterized protein / 0.662
3ldf SAHUncharacterized protein / 0.662
4uy6 SAHHistidine N-alpha-methyltransferase / 0.662
5f8f SFGPossible transcriptional regulatory protein / 0.661
2p35 SAHTrans-aconitate 2-methyltransferase / 0.660
4e2x SAHMethyltransferase / 0.660
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.659
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.658
5je2 SAHMethyl transferase / 0.658
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.657
4rvd SAMD-mycarose 3-C-methyltransferase / 0.657
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.655
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.655
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.654
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.653
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.653
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.653
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.652
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.652
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.651
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.650