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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
3axt SAM tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 1.171
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.994
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.779
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.759
1g60 SAMModification methylase MboII 2.1.1.72 0.758
2hnk SAHSAM-dependent O-methyltransferase / 0.748
2yxl SFG450aa long hypothetical fmu protein / 0.736
4dmg SAMUncharacterized protein / 0.727
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.723
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.722
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.720
4rtm SAMDNA adenine methylase 2.1.1.72 0.719
2cww SAHUncharacterized protein / 0.718
2g1p SAHDNA adenine methylase 2.1.1.72 0.717
3cbg SAHO-methyltransferase / 0.716
1eg2 MTAModification methylase RsrI 2.1.1.72 0.709
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.708
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.707
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.707
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.704
3ldg SAHUncharacterized protein / 0.703
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.703
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.702
1boo SAHModification methylase PvuII 2.1.1.113 0.701
3fpf MTAUncharacterized protein / 0.701
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.701
4rtk SAHDNA adenine methylase 2.1.1.72 0.701
1nw5 SAMModification methylase RsrI 2.1.1.72 0.699
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.699
3tos SAHCalS11 / 0.699
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.698
4rtp SAMDNA adenine methylase 2.1.1.72 0.697
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.695
1yf3 SAHDNA adenine methylase / 0.694
3duw SAHO-methyltransferase, putative / 0.694
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.693
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.692
1skm SAHModification methylase HhaI 2.1.1.37 0.691
4rtq SAHDNA adenine methylase 2.1.1.72 0.691
3m6w SAMRibosomal RNA small subunit methyltransferase F / 0.688
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.687
4oa5 SAHO-methyltransferase family protein / 0.686
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.683
4gf5 SAHCalS11 / 0.683
2zcj SAHModification methylase HhaI 2.1.1.37 0.682
3tm5 SFGUncharacterized protein / 0.679
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.679
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.678
2z6u SAHModification methylase HhaI 2.1.1.37 0.677
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.676
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.675
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.675
4gbe SAHDNA adenine methylase 2.1.1.72 0.675
10mh SAHModification methylase HhaI 2.1.1.37 0.672
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.671
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.670
3c3y SAHO-methyltransferase / 0.670
2ore SAHDNA adenine methylase 2.1.1.72 0.669
2f8l SAMLmo1582 protein / 0.668
2uyh SAHModification methylase HhaI 2.1.1.37 0.668
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.668
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.668
3eey SAMrRNA methylase / 0.667
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.667
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.666
2i9k SAHModification methylase HhaI 2.1.1.37 0.666
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.666
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.665
2br5 SAHCephalosporin hydroxylase CmcI / 0.664
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.664
4lwp SAHArginine N-methyltransferase, putative / 0.664
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.663
1af7 SAHChemotaxis protein methyltransferase 2.1.1.80 0.662
2eg5 SAH7-methylxanthosine synthase 1 / 0.662
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.662
3wdm ADN4-phosphopantoate--beta-alanine ligase 6.3.2.36 0.662
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.661
4rtj SFGDNA adenine methylase 2.1.1.72 0.661
1x1c SAHC-20 methyltransferase / 0.660
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.660
8mht SAHModification methylase HhaI 2.1.1.37 0.660
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.659
3ldf SAHUncharacterized protein / 0.658
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.658
3tr6 SAHO-methyltransferase / 0.658
4mht SAHModification methylase HhaI 2.1.1.37 0.658
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.658
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.658
4h0n SAHDnmt2 / 0.657
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.656
2zfu SAHRibosomal RNA-processing protein 8 / 0.656
3m6v SAMRibosomal RNA small subunit methyltransferase F / 0.656
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.656
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.656
3mht SAHModification methylase HhaI 2.1.1.37 0.655
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.655
4rtn SAHDNA adenine methylase 2.1.1.72 0.655
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.655
1fjx SAHModification methylase HhaI 2.1.1.37 0.654
5d4v SAHUncharacterized protein MJ0489 / 0.654
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.653
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.651
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.651
2plw SAMRibosomal RNA methyltransferase, putative / 0.650
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.650
3qv2 SAH5-cytosine DNA methyltransferase / 0.650
4rto SFGDNA adenine methylase 2.1.1.72 0.650