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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
3pt6 SAH 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
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.950
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.790
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.776
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.761
3ldg SAHUncharacterized protein / 0.757
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.745
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.744
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.738
2c7q SAHModification methylase HhaI 2.1.1.37 0.737
2yxl SFG450aa long hypothetical fmu protein / 0.737
3mht SAHModification methylase HhaI 2.1.1.37 0.736
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.733
2uyh SAHModification methylase HhaI 2.1.1.37 0.732
1skm SAHModification methylase HhaI 2.1.1.37 0.731
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.723
1fjx SAHModification methylase HhaI 2.1.1.37 0.722
10mh SAHModification methylase HhaI 2.1.1.37 0.716
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.713
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.712
4rtk SAHDNA adenine methylase 2.1.1.72 0.709
2z6u SAHModification methylase HhaI 2.1.1.37 0.700
1boo SAHModification methylase PvuII 2.1.1.113 0.699
2f8l SAMLmo1582 protein / 0.690
5je3 SAHMethyl transferase / 0.688
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.687
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.686
2g1p SAHDNA adenine methylase 2.1.1.72 0.686
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.684
2zcj SAHModification methylase HhaI 2.1.1.37 0.683
2i9k SAHModification methylase HhaI 2.1.1.37 0.682
4gbe SAHDNA adenine methylase 2.1.1.72 0.682
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.682
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.681
5jdz SAHMethyl transferase / 0.679
4dkj SAHCytosine-specific methyltransferase / 0.676
1yf3 SAHDNA adenine methylase / 0.674
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.672
3c3y SAHO-methyltransferase / 0.671
3go4 SAHUncharacterized protein / 0.671
4mht SAHModification methylase HhaI 2.1.1.37 0.671
4rtj SFGDNA adenine methylase 2.1.1.72 0.671
1nw5 SAMModification methylase RsrI 2.1.1.72 0.670
1mht SAHModification methylase HhaI 2.1.1.37 0.669
2hnk SAHSAM-dependent O-methyltransferase / 0.669
8mht SAHModification methylase HhaI 2.1.1.37 0.667
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.666
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.666
1eg2 MTAModification methylase RsrI 2.1.1.72 0.664
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.664
3lby SAHUncharacterized protein / 0.664
4da4 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.664
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.664
7mht SAHModification methylase HhaI 2.1.1.37 0.664
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.663
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.662
2zif SAMMethyltransferase / 0.661
4kvz SAHPtnL protein / 0.661
5mht SAHModification methylase HhaI 2.1.1.37 0.659
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.658
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.658
4kwc SAHMethyltransferase domain family / 0.658
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.657
2p35 SAHTrans-aconitate 2-methyltransferase / 0.657
4ft4 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.657
1aqi SAHModification methylase TaqI 2.1.1.72 0.656
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.656
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.655
5je2 SAHMethyl transferase / 0.654
9mht SAHModification methylase HhaI 2.1.1.37 0.654
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.653
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.652
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.652
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.652
2cww SAHUncharacterized protein / 0.651
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.651
4rtl SFGDNA adenine methylase 2.1.1.72 0.651
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.650
3m6v SAMRibosomal RNA small subunit methyltransferase F / 0.650