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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
3e8s SAH Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3e8s SAHUncharacterized protein / 1.178
3ou2 SAHSAM-dependent methyltransferase / 0.817
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.815
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.798
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.786
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.776
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.771
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.770
3e23 SAMUncharacterized protein / 0.766
4x3q SAHSibL / 0.765
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.764
4c04 SFGProtein arginine N-methyltransferase 6 / 0.763
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.761
3kkz SAMUncharacterized protein / 0.759
4c03 SFGProtein arginine N-methyltransferase 6 / 0.758
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.755
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.754
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.754
4nec SAHPutative SAM-dependent methyltransferase / 0.752
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.752
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.749
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.748
2yqz SAMUncharacterized protein / 0.746
3t0i SAHPutative methyltransferase / 0.744
3t7s SAMUncharacterized protein / 0.744
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.744
2qe6 SAMUncharacterized protein / 0.743
3fri SAH16S rRNA methylase / 0.742
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.741
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.740
3lst SAHCalO1 / 0.737
2xvm SAHTellurite methyltransferase 2.1.1.265 0.735
3ou6 SAMSAM-dependent methyltransferase / 0.735
5bp9 SAHPutative methyltransferase protein / 0.733
4hh4 SAHCcbJ / 0.730
3p9k SAHCaffeic acid O-methyltransferase / 0.729
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.728
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.728
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.728
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.727
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.727
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.725
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.722
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.722
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.721
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.719
2gs9 SAHUncharacterized protein / 0.718
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.718
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.717
1f3l SAHProtein arginine N-methyltransferase 3 / 0.713
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.712
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.711
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.711
4kwc SAHMethyltransferase domain family / 0.711
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.710
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.710
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.708
3c3y SAHO-methyltransferase / 0.707
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.706
4lwp SAHArginine N-methyltransferase, putative / 0.702
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.699
4rvd SAMD-mycarose 3-C-methyltransferase / 0.698
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.697
4uy6 SAHHistidine N-alpha-methyltransferase / 0.697
5je2 SAHMethyl transferase / 0.696
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.695
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.694
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.694
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.693
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.693
4kvz SAHPtnL protein / 0.693
5epe SAHUncharacterized protein / 0.693
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.691
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.691
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.690
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.690
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.689
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.689
5bp7 SAHSAM-dependent methyltransferase / 0.689
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.687
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.686
4pne SAHMethyltransferase-like protein / 0.686
3sxj SAMPutative methyltransferase / 0.685
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.684
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.684
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.682
4qpp SAHProtein arginine N-methyltransferase 6 / 0.682
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.681
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.681
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.680
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.679
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.679
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.677
1wy7 SAHUncharacterized protein / 0.677
5je3 SAHMethyl transferase / 0.677
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.676
2f8l SAMLmo1582 protein / 0.676
5f8f SFGPossible transcriptional regulatory protein / 0.676
3gu3 SAHMethyltransferase / 0.675
3lcc SAHThiocyanate methyltransferase 1 / 0.675
4g67 SAHUncharacterized ACR, COG1565 superfamily / 0.674
5jdz SAHMethyl transferase / 0.674
1yf3 SAHDNA adenine methylase / 0.673
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.673
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.670
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.670
3ua3 SAHProtein arginine N-methyltransferase 5 / 0.670
2p35 SAHTrans-aconitate 2-methyltransferase / 0.669
4e2x SAHMethyltransferase / 0.668
7mht SAHModification methylase HhaI 2.1.1.37 0.668
2fkn NADUrocanate hydratase 4.2.1.49 0.667
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.666
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.663
2uyh SAHModification methylase HhaI 2.1.1.37 0.663
3mht SAHModification methylase HhaI 2.1.1.37 0.661
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.661
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.661
4qnv GEKtRNA U34 carboxymethyltransferase / 0.661
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.660
2i9k SAHModification methylase HhaI 2.1.1.37 0.659
2z6u SAHModification methylase HhaI 2.1.1.37 0.659
2zcj SAHModification methylase HhaI 2.1.1.37 0.659
1orh SAHProtein arginine N-methyltransferase 1 / 0.658
2v7g NADUrocanate hydratase 4.2.1.49 0.658
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.657
3ldf SAHUncharacterized protein / 0.654
3lby SAHUncharacterized protein / 0.652
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.652
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.651