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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
5il1 SAM N6-adenosine-methyltransferase 70 kDa subunit

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 1.086
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.897
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.877
1nw5 SAMModification methylase RsrI 2.1.1.72 0.780
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.756
3tos SAHCalS11 / 0.731
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.711
1r6a SAHGenome polyprotein 2.7.7.48 0.710
4dmg SAMUncharacterized protein / 0.709
2g1p SAHDNA adenine methylase 2.1.1.72 0.708
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.707
4k6m SAHGenome polyprotein / 0.704
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.703
3evg SAHGenome polyprotein 2.1.1.56 0.702
4dkj SAHCytosine-specific methyltransferase / 0.702
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.698
2cww SAHUncharacterized protein / 0.694
2i9k SAHModification methylase HhaI 2.1.1.37 0.693
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.693
2p41 SAHGenome polyprotein / 0.692
4gf5 SAHCalS11 / 0.692
3ldg SAHUncharacterized protein / 0.691
4rtj SFGDNA adenine methylase 2.1.1.72 0.691
1fjx SAHModification methylase HhaI 2.1.1.37 0.690
3p8z SAHGenome polyprotein 2.1.1.56 0.690
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.687
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.687
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.687
4rtk SAHDNA adenine methylase 2.1.1.72 0.685
3p97 SAMGenome polyprotein 2.1.1.56 0.683
1yf3 SAHDNA adenine methylase / 0.681
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.681
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.681
4mb2 ATPUncharacterized protein / 0.681
2zif SAMMethyltransferase / 0.677
3eld SFGMethyltransferase / 0.676
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.676
4uck SAMLarge structural protein / 0.676
2zcj SAHModification methylase HhaI 2.1.1.37 0.675
5jjr SAHGenome polyprotein / 0.675
4poo SAMPutative RNA methylase / 0.674
3lkz SFGGenome polyprotein / 0.673
1nw6 SFGModification methylase RsrI 2.1.1.72 0.671
3evc SAHGenome polyprotein 2.1.1.56 0.671
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.671
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.670
4ctj SAMGenome polyprotein / 0.670
2p3q SAHGenome polyprotein / 0.668
2px2 SAHGenome polyprotein 2.7.7.48 0.668
3elu SAMMethyltransferase / 0.668
3emd SFGMethyltransferase / 0.668
3eva SAHGenome polyprotein 2.1.1.56 0.667
2pkm ADNAdenosine kinase 2.7.1.20 0.665
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.665
2ore SAHDNA adenine methylase 2.1.1.72 0.664
2px5 SAHGenome polyprotein 2.7.7.48 0.663
2yxl SFG450aa long hypothetical fmu protein / 0.663
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.662
3ou2 SAHSAM-dependent methyltransferase / 0.662
3qv2 SAH5-cytosine DNA methyltransferase / 0.662
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.662
2uyh SAHModification methylase HhaI 2.1.1.37 0.660
4rtm SAMDNA adenine methylase 2.1.1.72 0.660
3m6w SAMRibosomal RNA small subunit methyltransferase F / 0.658
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.658
2hmy SAMModification methylase HhaI 2.1.1.37 0.657
7mht SAHModification methylase HhaI 2.1.1.37 0.655
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.654
5je4 SAHMethyl transferase / 0.654
2h39 ADQADP-glucose phosphorylase / 0.653
2zdy ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2 0.652
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.652
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.651
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.650
3mht SAHModification methylase HhaI 2.1.1.37 0.650