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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
3sr4 TT8 Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 1.125
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.976
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.956
5bxy SAHPutative RNA methylase family UPF0020 / 0.832
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.810
5je2 SAHMethyl transferase / 0.799
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.782
4hh4 SAHCcbJ / 0.781
3go4 SAHUncharacterized protein / 0.777
2qe6 SAMUncharacterized protein / 0.762
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.759
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.758
4lwp SAHArginine N-methyltransferase, putative / 0.758
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.757
1f3l SAHProtein arginine N-methyltransferase 3 / 0.754
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.749
5je3 SAHMethyl transferase / 0.749
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.742
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.739
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.739
5jdz SAHMethyl transferase / 0.739
3lcc SAHThiocyanate methyltransferase 1 / 0.738
4er6 AW2Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.738
4qpp SAHProtein arginine N-methyltransferase 6 / 0.738
5je4 SAHMethyl transferase / 0.732
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.731
2p35 SAHTrans-aconitate 2-methyltransferase / 0.729
1ori SAHProtein arginine N-methyltransferase 1 / 0.725
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.724
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.724
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.722
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.721
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.719
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.718
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.717
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.716
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.715
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.714
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.713
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.712
4kvz SAHPtnL protein / 0.711
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.708
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.708
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.707
4kwc SAHMethyltransferase domain family / 0.707
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.705
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.704
2i9k SAHModification methylase HhaI 2.1.1.37 0.703
2xvm SAHTellurite methyltransferase 2.1.1.265 0.703
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.703
3tm4 SAMUncharacterized protein / 0.703
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.702
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.702
4rtk SAHDNA adenine methylase 2.1.1.72 0.701
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.699
3mht SAHModification methylase HhaI 2.1.1.37 0.699
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.697
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.697
1eg2 MTAModification methylase RsrI 2.1.1.72 0.696
1orh SAHProtein arginine N-methyltransferase 1 / 0.696
3t7s SAMUncharacterized protein / 0.695
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.694
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.693
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.692
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.692
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.692
3kkz SAMUncharacterized protein / 0.691
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.690
2eg5 SAH7-methylxanthosine synthase 1 / 0.689
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.689
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.689
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.687
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.687
5bp9 SAHPutative methyltransferase protein / 0.687
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.686
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.686
3ldg SAHUncharacterized protein / 0.686
3tm5 SFGUncharacterized protein / 0.686
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.686
3t7t SAHUncharacterized protein / 0.685
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.684
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.684
2zbp SAMRibosomal protein L11 methyltransferase 2.1.1 0.684
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.684
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.683
3c3y SAHO-methyltransferase / 0.683
1wy7 SAHUncharacterized protein / 0.682
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.682
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.682
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.681
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.681
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.680
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.680
5f8f SFGPossible transcriptional regulatory protein / 0.679
2ih2 NEAModification methylase TaqI 2.1.1.72 0.678
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.676
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.676
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.676
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.676
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.675
4nec SAHPutative SAM-dependent methyltransferase / 0.675
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.675
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.674
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.673
3tos SAHCalS11 / 0.673
4yac NAIC alpha-dehydrogenase / 0.673
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.672
2v7g NADUrocanate hydratase 4.2.1.49 0.671
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.671
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.671
3lst SAHCalO1 / 0.670
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.670
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.669
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.669
2z6u SAHModification methylase HhaI 2.1.1.37 0.669
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.668
4pgh SAMCaffeic acid O-methyltransferase / 0.668
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.668
3p9c SAHCaffeic acid O-methyltransferase / 0.667
3vyw SAMUncharacterized protein / 0.667
4er7 AW3Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.667
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.665
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.665
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.665
4ce0 SAHProbable O-methyltransferase / 0.665
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.665
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.664
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.664
3geg NADShort-chain dehydrogenase/reductase SDR / 0.664
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.664
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.663
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.663
3eey SAMrRNA methylase / 0.663
4c04 SFGProtein arginine N-methyltransferase 6 / 0.663
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.662
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.662
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.662
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.660
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.660
3ndr NADPyridoxal 4-dehydrogenase 1.1.1.107 0.660
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.659
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.659
2hnk SAHSAM-dependent O-methyltransferase / 0.658
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.657
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.656
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.655
5bw4 SAMUncharacterized protein / 0.655
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.654
1skm SAHModification methylase HhaI 2.1.1.37 0.654
7mht SAHModification methylase HhaI 2.1.1.37 0.654
2yxl SFG450aa long hypothetical fmu protein / 0.653
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.653
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.653
2yqz SAMUncharacterized protein / 0.652
3t0i SAHPutative methyltransferase / 0.652
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.652
4qnu GEKtRNA U34 carboxymethyltransferase / 0.652
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.651
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.651
4m55 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.651
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.651
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.650
4c05 SAHProtein arginine N-methyltransferase 6 / 0.650
4id9 NADPutative UDP-glucose 4-epimerase / 0.650
5eku SAHArginine N-methyltransferase, putative / 0.650