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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
3swr SFG DNA (cytosine-5)-methyltransferase 1 2.1.1.37

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 1.003
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.801
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.776
1yf3 SAHDNA adenine methylase / 0.771
2c7q SAHModification methylase HhaI 2.1.1.37 0.769
2yxl SFG450aa long hypothetical fmu protein / 0.762
2z6u SAHModification methylase HhaI 2.1.1.37 0.757
1skm SAHModification methylase HhaI 2.1.1.37 0.752
3mht SAHModification methylase HhaI 2.1.1.37 0.747
1g60 SAMModification methylase MboII 2.1.1.72 0.745
2zcj SAHModification methylase HhaI 2.1.1.37 0.742
3tm4 SAMUncharacterized protein / 0.742
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.735
2uyh SAHModification methylase HhaI 2.1.1.37 0.734
2i9k SAHModification methylase HhaI 2.1.1.37 0.725
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.720
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.719
4mht SAHModification methylase HhaI 2.1.1.37 0.716
10mh SAHModification methylase HhaI 2.1.1.37 0.715
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.712
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.710
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.705
2g1p SAHDNA adenine methylase 2.1.1.72 0.705
2f8l SAMLmo1582 protein / 0.700
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.699
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.696
8mht SAHModification methylase HhaI 2.1.1.37 0.695
1boo SAHModification methylase PvuII 2.1.1.113 0.694
1nw5 SAMModification methylase RsrI 2.1.1.72 0.694
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.694
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.693
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.693
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.693
5mht SAHModification methylase HhaI 2.1.1.37 0.692
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.690
7mht SAHModification methylase HhaI 2.1.1.37 0.690
3ldg SAHUncharacterized protein / 0.687
9mht SAHModification methylase HhaI 2.1.1.37 0.687
3tm5 SFGUncharacterized protein / 0.686
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.683
4gbe SAHDNA adenine methylase 2.1.1.72 0.683
5je3 SAHMethyl transferase / 0.679
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.676
3ldf SAHUncharacterized protein / 0.676
4rtj SFGDNA adenine methylase 2.1.1.72 0.676
2px2 SAHGenome polyprotein 2.7.7.48 0.675
3tlj SAHUncharacterized protein / 0.675
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.670
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.670
3ely SAHMethyltransferase / 0.669
2zif SAMMethyltransferase / 0.667
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.667
4rtq SAHDNA adenine methylase 2.1.1.72 0.666
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.665
4rtk SAHDNA adenine methylase 2.1.1.72 0.665
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.659
3tr6 SAHO-methyltransferase / 0.658
1ve3 SAMUncharacterized protein / 0.656
4dkj SAHCytosine-specific methyltransferase / 0.656
1eg2 MTAModification methylase RsrI 2.1.1.72 0.655
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.654
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.654
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.653
5je4 SAHMethyl transferase / 0.653
1v59 NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.652
4mb2 ATPUncharacterized protein / 0.652
4rtl SFGDNA adenine methylase 2.1.1.72 0.652
4ctj SAMGenome polyprotein / 0.651
4yv2 S4MSpermidine synthase, putative / 0.651
5jjr SAHGenome polyprotein / 0.651
3evg SAHGenome polyprotein 2.1.1.56 0.650
3lby SAHUncharacterized protein / 0.650
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.650