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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
3qow SAM 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
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 1.062
3sr4 TT8Histone-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 0.974
5bxy SAHPutative RNA methylase family UPF0020 / 0.813
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.792
5je2 SAHMethyl transferase / 0.784
5jdz SAHMethyl transferase / 0.778
5je3 SAHMethyl transferase / 0.777
2yqz SAMUncharacterized protein / 0.774
3go4 SAHUncharacterized protein / 0.774
4hh4 SAHCcbJ / 0.774
5je4 SAHMethyl transferase / 0.768
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.761
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.757
3lcc SAHThiocyanate methyltransferase 1 / 0.756
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.750
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.750
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.749
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.748
2qe6 SAMUncharacterized protein / 0.746
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.740
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.737
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.735
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.734
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.732
4lwp SAHArginine N-methyltransferase, putative / 0.731
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.730
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.728
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.725
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.724
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.723
3tm4 SAMUncharacterized protein / 0.723
4qpp SAHProtein arginine N-methyltransferase 6 / 0.723
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.717
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.716
3tm5 SFGUncharacterized protein / 0.716
3fri SAH16S rRNA methylase / 0.715
4c03 SFGProtein arginine N-methyltransferase 6 / 0.713
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.713
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.712
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.712
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.710
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.709
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.708
1skm SAHModification methylase HhaI 2.1.1.37 0.707
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.706
2xvm SAHTellurite methyltransferase 2.1.1.265 0.706
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.706
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.706
3ou2 SAHSAM-dependent methyltransferase / 0.704
1f3l SAHProtein arginine N-methyltransferase 3 / 0.703
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.703
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.703
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.702
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.702
2np6 NEAModification methylase TaqI 2.1.1.72 0.701
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.701
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.700
4rtk SAHDNA adenine methylase 2.1.1.72 0.699
3lst SAHCalO1 / 0.698
2ih2 NEAModification methylase TaqI 2.1.1.72 0.697
3t7t SAHUncharacterized protein / 0.697
4c04 SFGProtein arginine N-methyltransferase 6 / 0.697
2yxl SFG450aa long hypothetical fmu protein / 0.695
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.695
3kkz SAMUncharacterized protein / 0.695
3ldg SAHUncharacterized protein / 0.695
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.694
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.694
2i9k SAHModification methylase HhaI 2.1.1.37 0.693
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.693
5f8f SFGPossible transcriptional regulatory protein / 0.693
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.692
2ih5 NEAModification methylase TaqI 2.1.1.72 0.692
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.691
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.691
3t7s SAMUncharacterized protein / 0.691
1g1a NADdTDP-glucose 4,6-dehydratase / 0.690
1orh SAHProtein arginine N-methyltransferase 1 / 0.690
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.690
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.690
2p35 SAHTrans-aconitate 2-methyltransferase / 0.689
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.688
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.688
3mht SAHModification methylase HhaI 2.1.1.37 0.688
1ori SAHProtein arginine N-methyltransferase 1 / 0.687
2o06 MTASpermidine synthase 2.5.1.16 0.687
2g1p SAHDNA adenine methylase 2.1.1.72 0.686
4kwc SAHMethyltransferase domain family / 0.686
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.685
4er6 AW2Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.683
4kvz SAHPtnL protein / 0.683
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.683
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.682
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.682
2f8l SAMLmo1582 protein / 0.681
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.681
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.679
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.677
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.676
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.675
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.675
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.675
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.675
2c7q SAHModification methylase HhaI 2.1.1.37 0.674
2zif SAMMethyltransferase / 0.674
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.673
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.673
2z6u SAHModification methylase HhaI 2.1.1.37 0.673
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.673
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.673
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.672
1boo SAHModification methylase PvuII 2.1.1.113 0.671
3e23 SAMUncharacterized protein / 0.671
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.671
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.671
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.670
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.670
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.668
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.668
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.668
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.668
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.667
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.665
3ko8 NADNAD-dependent epimerase/dehydratase / 0.665
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.665
4id9 NADPutative UDP-glucose 4-epimerase / 0.665
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.665
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.664
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.664
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.664
4ce0 SAHProbable O-methyltransferase / 0.664
4er7 AW3Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.664
5bp7 SAHSAM-dependent methyltransferase / 0.664
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.663
2c20 NADUDP-glucose 4-epimerase / 0.662
5epe SAHUncharacterized protein / 0.662
7mht SAHModification methylase HhaI 2.1.1.37 0.662
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.661
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.661
4tlx FDAKtzI / 0.661
3p9k SAHCaffeic acid O-methyltransferase / 0.660
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.659
4g56 SAHProtein arginine N-methyltransferase 5 / 0.659
4rtj SFGDNA adenine methylase 2.1.1.72 0.659
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.657
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.657
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.657
4oa5 SAHO-methyltransferase family protein / 0.657
2oah QINBeta-secretase 1 3.4.23.46 0.656
5br7 FADUDP-galactopyranose mutase / 0.656
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.655
4tm4 FDAKtzI / 0.655
1g38 NEAModification methylase TaqI 2.1.1.72 0.654
2eg5 SAH7-methylxanthosine synthase 1 / 0.654
2uyh SAHModification methylase HhaI 2.1.1.37 0.654
4ctk SAMGenome polyprotein / 0.654
5eku SAHArginine N-methyltransferase, putative / 0.654
4yag NAIC alpha-dehydrogenase / 0.653
3lhd SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.652
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.652
3ndr NADPyridoxal 4-dehydrogenase 1.1.1.107 0.651
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.651