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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
4dcm SAM Ribosomal RNA large subunit methyltransferase G 2.1.1.174

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 1.054
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.836
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.803
3ou2 SAHSAM-dependent methyltransferase / 0.801
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.800
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.799
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.798
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.790
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.779
3ldg SAHUncharacterized protein / 0.769
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.762
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.760
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.759
4hh4 SAHCcbJ / 0.759
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.753
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.750
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.749
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.748
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.747
1nw5 SAMModification methylase RsrI 2.1.1.72 0.744
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.739
3tm4 SAMUncharacterized protein / 0.737
2p35 SAHTrans-aconitate 2-methyltransferase / 0.736
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.732
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.732
1ori SAHProtein arginine N-methyltransferase 1 / 0.730
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.729
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.728
2g1p SAHDNA adenine methylase 2.1.1.72 0.726
4rtk SAHDNA adenine methylase 2.1.1.72 0.726
2z6u SAHModification methylase HhaI 2.1.1.37 0.725
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.724
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.721
4kwc SAHMethyltransferase domain family / 0.720
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.720
5je2 SAHMethyl transferase / 0.716
1eg2 MTAModification methylase RsrI 2.1.1.72 0.715
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.715
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.714
4kvz SAHPtnL protein / 0.713
4nec SAHPutative SAM-dependent methyltransferase / 0.713
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.713
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.712
2c7q SAHModification methylase HhaI 2.1.1.37 0.711
2f8l SAMLmo1582 protein / 0.711
2i9k SAHModification methylase HhaI 2.1.1.37 0.711
3lcc SAHThiocyanate methyltransferase 1 / 0.710
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.710
3mht SAHModification methylase HhaI 2.1.1.37 0.708
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.707
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.706
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.706
2yqz SAMUncharacterized protein / 0.706
3kkz SAMUncharacterized protein / 0.704
1skm SAHModification methylase HhaI 2.1.1.37 0.703
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.703
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.703
3p9k SAHCaffeic acid O-methyltransferase / 0.703
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.702
5bp9 SAHPutative methyltransferase protein / 0.702
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.701
5jdz SAHMethyl transferase / 0.701
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.700
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.700
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.699
5je4 SAHMethyl transferase / 0.699
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.698
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.696
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.696
4c04 SFGProtein arginine N-methyltransferase 6 / 0.695
2uyh SAHModification methylase HhaI 2.1.1.37 0.694
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.694
7mht SAHModification methylase HhaI 2.1.1.37 0.694
3e8s SAHUncharacterized protein / 0.693
3ua3 SAHProtein arginine N-methyltransferase 5 / 0.693
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.693
2hmv ADPKtr system potassium uptake protein A / 0.692
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.692
4c03 SFGProtein arginine N-methyltransferase 6 / 0.690
4rtq SAHDNA adenine methylase 2.1.1.72 0.690
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.689
10mh SAHModification methylase HhaI 2.1.1.37 0.688
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.688
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.688
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.688
2ore SAHDNA adenine methylase 2.1.1.72 0.688
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.688
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.688
3t0i SAHPutative methyltransferase / 0.687
4pgh SAMCaffeic acid O-methyltransferase / 0.687
1orh SAHProtein arginine N-methyltransferase 1 / 0.686
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.685
2yxl SFG450aa long hypothetical fmu protein / 0.683
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.683
3p9c SAHCaffeic acid O-methyltransferase / 0.683
4uy6 SAHHistidine N-alpha-methyltransferase / 0.683
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.681
2zif SAMMethyltransferase / 0.681
2o06 MTASpermidine synthase 2.5.1.16 0.679
2zcj SAHModification methylase HhaI 2.1.1.37 0.678
3go4 SAHUncharacterized protein / 0.678
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.678
3tos SAHCalS11 / 0.678
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.677
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.677
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.676
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.675
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.675
3lst SAHCalO1 / 0.674
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.674
1fjx SAHModification methylase HhaI 2.1.1.37 0.673
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.673
4c05 SAHProtein arginine N-methyltransferase 6 / 0.673
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.672
4rtj SFGDNA adenine methylase 2.1.1.72 0.670
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.668
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.667
2xvm SAHTellurite methyltransferase 2.1.1.265 0.667
2zfu SAHRibosomal RNA-processing protein 8 / 0.667
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.667
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.666
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.665
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.664
4lwp SAHArginine N-methyltransferase, putative / 0.664
1nw6 SFGModification methylase RsrI 2.1.1.72 0.662
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.662
2ibt NEAModification methylase TaqI 2.1.1.72 0.662
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.662
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.661
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.661
3lby SAHUncharacterized protein / 0.661
3rw9 DSHSpermidine synthase 2.5.1.16 0.661
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.660
3abi NADUncharacterized protein / 0.660
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.660
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.660
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.660
9mht SAHModification methylase HhaI 2.1.1.37 0.660
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.659
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.659
5bxy SAHPutative RNA methylase family UPF0020 / 0.659
2px2 SAHGenome polyprotein 2.7.7.48 0.658
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.658
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.658
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.658
4dmg SAMUncharacterized protein / 0.658
4rtr SAMDNA adenine methylase 2.1.1.72 0.658
3qv2 SAH5-cytosine DNA methyltransferase / 0.657
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.657
1vq1 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.656
3wdm ADN4-phosphopantoate--beta-alanine ligase 6.3.2.36 0.656
4g56 SAHProtein arginine N-methyltransferase 5 / 0.656
2eg5 SAH7-methylxanthosine synthase 1 / 0.655
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.655
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.655
4gf5 SAHCalS11 / 0.654
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.654
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.653
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.653
4ctk SAMGenome polyprotein / 0.653
4rvd SAMD-mycarose 3-C-methyltransferase / 0.653
1aqi SAHModification methylase TaqI 2.1.1.72 0.652
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.652
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.652
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.652
4gbe SAHDNA adenine methylase 2.1.1.72 0.652
3e23 SAMUncharacterized protein / 0.651
4ft4 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.651
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.651
4rtm SAMDNA adenine methylase 2.1.1.72 0.651
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.651
1pow FADPyruvate oxidase 1.2.3.3 0.650
2hms NAIKtr system potassium uptake protein A / 0.650
3wv7 ADPHmd co-occurring protein HcgE / 0.650