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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
5e72 SAM N2, N2-dimethylguanosine tRNA methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 1.070
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.806
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.768
2ore SAHDNA adenine methylase 2.1.1.72 0.765
4gbe SAHDNA adenine methylase 2.1.1.72 0.764
5bxy SAHPutative RNA methylase family UPF0020 / 0.764
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.761
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.750
2yxl SFG450aa long hypothetical fmu protein / 0.746
3ldf SAHUncharacterized protein / 0.745
3lcc SAHThiocyanate methyltransferase 1 / 0.742
1nw6 SFGModification methylase RsrI 2.1.1.72 0.741
2z6u SAHModification methylase HhaI 2.1.1.37 0.739
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.739
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.735
3mht SAHModification methylase HhaI 2.1.1.37 0.732
1skm SAHModification methylase HhaI 2.1.1.37 0.730
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.730
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.728
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.725
2uyh SAHModification methylase HhaI 2.1.1.37 0.724
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.724
1boo SAHModification methylase PvuII 2.1.1.113 0.722
3ldg SAHUncharacterized protein / 0.720
4rtk SAHDNA adenine methylase 2.1.1.72 0.720
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.718
4dmg SAMUncharacterized protein / 0.717
4lwp SAHArginine N-methyltransferase, putative / 0.717
5bp9 SAHPutative methyltransferase protein / 0.717
1eg2 MTAModification methylase RsrI 2.1.1.72 0.716
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.716
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.716
1nw5 SAMModification methylase RsrI 2.1.1.72 0.715
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.714
1g60 SAMModification methylase MboII 2.1.1.72 0.710
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.710
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.708
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.707
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.706
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.704
10mh SAHModification methylase HhaI 2.1.1.37 0.701
7mht SAHModification methylase HhaI 2.1.1.37 0.701
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.700
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.699
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.699
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.699
2g1p SAHDNA adenine methylase 2.1.1.72 0.697
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.696
2hmv ADPKtr system potassium uptake protein A / 0.696
2zif SAMMethyltransferase / 0.696
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.696
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.695
4rtj SFGDNA adenine methylase 2.1.1.72 0.695
2c7q SAHModification methylase HhaI 2.1.1.37 0.693
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.693
4c03 SFGProtein arginine N-methyltransferase 6 / 0.693
4yv2 S4MSpermidine synthase, putative / 0.693
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.692
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.692
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.691
4rts SAMDNA adenine methylase 2.1.1.72 0.691
1f3l SAHProtein arginine N-methyltransferase 3 / 0.690
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.690
4rto SFGDNA adenine methylase 2.1.1.72 0.690
5epe SAHUncharacterized protein / 0.690
1fjx SAHModification methylase HhaI 2.1.1.37 0.689
3t7s SAMUncharacterized protein / 0.689
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.688
4rtm SAMDNA adenine methylase 2.1.1.72 0.688
2hnk SAHSAM-dependent O-methyltransferase / 0.687
3go4 SAHUncharacterized protein / 0.687
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.686
1yf3 SAHDNA adenine methylase / 0.685
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.685
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.685
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.684
2o06 MTASpermidine synthase 2.5.1.16 0.684
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.684
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.682
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.682
4kvz SAHPtnL protein / 0.682
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.682
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.681
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.681
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.681
3duw SAHO-methyltransferase, putative / 0.681
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.680
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.680
4nec SAHPutative SAM-dependent methyltransferase / 0.680
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.680
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.680
5eku SAHArginine N-methyltransferase, putative / 0.680
5je2 SAHMethyl transferase / 0.680
1mht SAHModification methylase HhaI 2.1.1.37 0.679
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.679
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.679
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.679
1y9d FADPyruvate oxidase 1.2.3.3 0.678
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.677
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.677
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.677
4c05 SAHProtein arginine N-methyltransferase 6 / 0.676
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.676
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.675
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.675
4hh4 SAHCcbJ / 0.674
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.673
2zcj SAHModification methylase HhaI 2.1.1.37 0.673
3tm4 SAMUncharacterized protein / 0.673
4rtp SAMDNA adenine methylase 2.1.1.72 0.672
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.671
2i9k SAHModification methylase HhaI 2.1.1.37 0.671
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.671
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.671
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.671
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.670
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.670
2yqz SAMUncharacterized protein / 0.670
4gol SA8DNA adenine methylase 2.1.1.72 0.670
4kwc SAHMethyltransferase domain family / 0.670
1aqi SAHModification methylase TaqI 2.1.1.72 0.668
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.668
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.668
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.668
3rw9 DSHSpermidine synthase 2.5.1.16 0.667
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.667
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.667
2p35 SAHTrans-aconitate 2-methyltransferase / 0.666
3cbg SAHO-methyltransferase / 0.666
4poo SAMPutative RNA methylase / 0.666
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.665
1pow FADPyruvate oxidase 1.2.3.3 0.664
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.664
3kkz SAMUncharacterized protein / 0.664
4rtn SAHDNA adenine methylase 2.1.1.72 0.664
4h0n SAHDnmt2 / 0.663
5jdz SAHMethyl transferase / 0.663
1jkf NADInositol-3-phosphate synthase 5.5.1.4 0.662
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.662
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.662
5je3 SAHMethyl transferase / 0.662
5mht SAHModification methylase HhaI 2.1.1.37 0.662
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.661
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.660
2cww SAHUncharacterized protein / 0.660
2f8l SAMLmo1582 protein / 0.660
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.660
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.659
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.659
3p9c SAHCaffeic acid O-methyltransferase / 0.658
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.657
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.657
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.657
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.657
4qpp SAHProtein arginine N-methyltransferase 6 / 0.657
2p5u NADUDP-glucose 4-epimerase / 0.655
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.654
1x1c SAHC-20 methyltransferase / 0.654
4gc9 SAMDimethyladenosine transferase 1, mitochondrial 2.1.1 0.654
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.654
4mb2 ATPUncharacterized protein / 0.654
9mht SAHModification methylase HhaI 2.1.1.37 0.654
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.653
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.652
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.652
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.652
4em4 FADCoenzyme A disulfide reductase / 0.652
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.651
4oa5 SAHO-methyltransferase family protein / 0.651
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.651
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.650
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.650
3tos SAHCalS11 / 0.650
4eqg A5AHistidine triad nucleotide-binding protein 1 3 0.650