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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
4dkj SAH Cytosine-specific methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4dkj SAHCytosine-specific methyltransferase / 1.068
2c7q SAHModification methylase HhaI 2.1.1.37 0.817
2i9k SAHModification methylase HhaI 2.1.1.37 0.815
1skm SAHModification methylase HhaI 2.1.1.37 0.808
10mh SAHModification methylase HhaI 2.1.1.37 0.788
2uyh SAHModification methylase HhaI 2.1.1.37 0.786
2z6u SAHModification methylase HhaI 2.1.1.37 0.784
7mht SAHModification methylase HhaI 2.1.1.37 0.784
2zcj SAHModification methylase HhaI 2.1.1.37 0.780
5mht SAHModification methylase HhaI 2.1.1.37 0.766
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.758
1fjx SAHModification methylase HhaI 2.1.1.37 0.746
3qv2 SAH5-cytosine DNA methyltransferase / 0.740
3mht SAHModification methylase HhaI 2.1.1.37 0.736
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.730
3c3y SAHO-methyltransferase / 0.724
4mht SAHModification methylase HhaI 2.1.1.37 0.723
9mht SAHModification methylase HhaI 2.1.1.37 0.721
1yf3 SAHDNA adenine methylase / 0.719
3ldg SAHUncharacterized protein / 0.714
1eg2 MTAModification methylase RsrI 2.1.1.72 0.712
1mht SAHModification methylase HhaI 2.1.1.37 0.710
1nw5 SAMModification methylase RsrI 2.1.1.72 0.710
4poo SAMPutative RNA methylase / 0.704
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.702
4c03 SFGProtein arginine N-methyltransferase 6 / 0.701
3ou6 SAMSAM-dependent methyltransferase / 0.699
3ou2 SAHSAM-dependent methyltransferase / 0.695
1g60 SAMModification methylase MboII 2.1.1.72 0.693
2cww SAHUncharacterized protein / 0.693
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.691
3lby SAHUncharacterized protein / 0.689
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.688
2hmy SAMModification methylase HhaI 2.1.1.37 0.685
3eey SAMrRNA methylase / 0.684
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.683
3tos SAHCalS11 / 0.682
2eg5 SAH7-methylxanthosine synthase 1 / 0.680
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.680
4gf5 SAHCalS11 / 0.680
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.679
2g1p SAHDNA adenine methylase 2.1.1.72 0.679
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.679
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.679
2bm9 SAMCephalosporin hydroxylase CmcI / 0.678
4gbe SAHDNA adenine methylase 2.1.1.72 0.678
4nec SAHPutative SAM-dependent methyltransferase / 0.678
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.676
4rtk SAHDNA adenine methylase 2.1.1.72 0.676
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.675
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.674
2yxl SFG450aa long hypothetical fmu protein / 0.673
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.673
2qe6 SAMUncharacterized protein / 0.672
3tlj SAHUncharacterized protein / 0.671
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.670
3tm4 SAMUncharacterized protein / 0.670
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.670
5je4 SAHMethyl transferase / 0.670
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.669
3go4 SAHUncharacterized protein / 0.668
5je2 SAHMethyl transferase / 0.667
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.667
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.666
4h0n SAHDnmt2 / 0.666
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.663
2ore SAHDNA adenine methylase 2.1.1.72 0.663
3cbg SAHO-methyltransferase / 0.663
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.663
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.662
4rtj SFGDNA adenine methylase 2.1.1.72 0.662
3ldf SAHUncharacterized protein / 0.661
4rto SFGDNA adenine methylase 2.1.1.72 0.661
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.660
8mht SAHModification methylase HhaI 2.1.1.37 0.660
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.658
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.658
4rtl SFGDNA adenine methylase 2.1.1.72 0.657
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.656
4kvz SAHPtnL protein / 0.656
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.655
3m6w SAMRibosomal RNA small subunit methyltransferase F / 0.655
4pne SAHMethyltransferase-like protein / 0.655
5bp7 SAHSAM-dependent methyltransferase / 0.654
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.653
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.652
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.652
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.651
3s55 NADPutative short-chain dehydrogenase/reductase / 0.651
4rtm SAMDNA adenine methylase 2.1.1.72 0.651
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.650
2plw SAMRibosomal RNA methyltransferase, putative / 0.650
3e23 SAMUncharacterized protein / 0.650
4rvd SAMD-mycarose 3-C-methyltransferase / 0.650