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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
3qv2 SAH 5-cytosine DNA methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3qv2 SAH5-cytosine DNA methyltransferase / 0.936
9mht SAHModification methylase HhaI 2.1.1.37 0.774
10mh SAHModification methylase HhaI 2.1.1.37 0.769
5mht SAHModification methylase HhaI 2.1.1.37 0.766
1mht SAHModification methylase HhaI 2.1.1.37 0.760
2uyh SAHModification methylase HhaI 2.1.1.37 0.756
7mht SAHModification methylase HhaI 2.1.1.37 0.753
2c7q SAHModification methylase HhaI 2.1.1.37 0.741
4dkj SAHCytosine-specific methyltransferase / 0.740
1yf3 SAHDNA adenine methylase / 0.739
4mht SAHModification methylase HhaI 2.1.1.37 0.738
2zcj SAHModification methylase HhaI 2.1.1.37 0.729
3mht SAHModification methylase HhaI 2.1.1.37 0.727
2z6u SAHModification methylase HhaI 2.1.1.37 0.725
1skm SAHModification methylase HhaI 2.1.1.37 0.724
1nw5 SAMModification methylase RsrI 2.1.1.72 0.718
4gbe SAHDNA adenine methylase 2.1.1.72 0.715
4rtk SAHDNA adenine methylase 2.1.1.72 0.711
4poo SAMPutative RNA methylase / 0.709
4rtj SFGDNA adenine methylase 2.1.1.72 0.709
4rtm SAMDNA adenine methylase 2.1.1.72 0.709
8mht SAHModification methylase HhaI 2.1.1.37 0.709
3tm5 SFGUncharacterized protein / 0.706
3ldg SAHUncharacterized protein / 0.702
4rtl SFGDNA adenine methylase 2.1.1.72 0.702
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.701
3tm4 SAMUncharacterized protein / 0.694
1eg2 MTAModification methylase RsrI 2.1.1.72 0.692
1fjx SAHModification methylase HhaI 2.1.1.37 0.692
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.691
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.691
3ou2 SAHSAM-dependent methyltransferase / 0.687
4dmg SAMUncharacterized protein / 0.686
3ou6 SAMSAM-dependent methyltransferase / 0.680
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.678
1g60 SAMModification methylase MboII 2.1.1.72 0.677
3c3y SAHO-methyltransferase / 0.674
2hmy SAMModification methylase HhaI 2.1.1.37 0.673
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.672
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.672
4rtp SAMDNA adenine methylase 2.1.1.72 0.671
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.671
1af7 SAHChemotaxis protein methyltransferase 2.1.1.80 0.670
2i9k SAHModification methylase HhaI 2.1.1.37 0.668
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.667
2zif SAMMethyltransferase / 0.666
2cww SAHUncharacterized protein / 0.665
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.665
2br5 SAHCephalosporin hydroxylase CmcI / 0.664
2eg5 SAH7-methylxanthosine synthase 1 / 0.664
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.664
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.662
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.662
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.662
2g1p SAHDNA adenine methylase 2.1.1.72 0.660
3eey SAMrRNA methylase / 0.659
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.658
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.658
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.658
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.657
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.655
2pxa SAHGenome polyprotein 2.7.7.48 0.654
4yuz S4MSpermidine synthase, putative / 0.653
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.652
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.652
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.652
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.650