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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
2zif SAM Methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2zif SAMMethyltransferase / 1.027
1nw5 SAMModification methylase RsrI 2.1.1.72 0.751
1skm SAHModification methylase HhaI 2.1.1.37 0.746
2i9k SAHModification methylase HhaI 2.1.1.37 0.737
2zcj SAHModification methylase HhaI 2.1.1.37 0.736
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.735
7mht SAHModification methylase HhaI 2.1.1.37 0.735
1eg2 MTAModification methylase RsrI 2.1.1.72 0.733
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.733
2uyh SAHModification methylase HhaI 2.1.1.37 0.728
2g1p SAHDNA adenine methylase 2.1.1.72 0.717
10mh SAHModification methylase HhaI 2.1.1.37 0.716
2z6u SAHModification methylase HhaI 2.1.1.37 0.716
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.715
3ldg SAHUncharacterized protein / 0.715
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.713
3mht SAHModification methylase HhaI 2.1.1.37 0.713
4rtk SAHDNA adenine methylase 2.1.1.72 0.713
2c7q SAHModification methylase HhaI 2.1.1.37 0.708
5mht SAHModification methylase HhaI 2.1.1.37 0.706
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.704
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.698
3e23 SAMUncharacterized protein / 0.698
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.697
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.696
2ore SAHDNA adenine methylase 2.1.1.72 0.694
1nw6 SFGModification methylase RsrI 2.1.1.72 0.690
3tm4 SAMUncharacterized protein / 0.690
2f8l SAMLmo1582 protein / 0.688
4gbe SAHDNA adenine methylase 2.1.1.72 0.687
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.687
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.687
1g60 SAMModification methylase MboII 2.1.1.72 0.686
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.686
4c04 SFGProtein arginine N-methyltransferase 6 / 0.685
4dmg SAMUncharacterized protein / 0.684
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.683
1boo SAHModification methylase PvuII 2.1.1.113 0.682
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.682
2px2 SAHGenome polyprotein 2.7.7.48 0.681
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.681
3tlj SAHUncharacterized protein / 0.680
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.680
3tm5 SFGUncharacterized protein / 0.679
4mht SAHModification methylase HhaI 2.1.1.37 0.678
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.677
9mht SAHModification methylase HhaI 2.1.1.37 0.675
2yxl SFG450aa long hypothetical fmu protein / 0.674
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.674
3ldf SAHUncharacterized protein / 0.673
3cbg SAHO-methyltransferase / 0.672
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.670
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.670
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.668
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.667
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.667
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.666
3qv2 SAH5-cytosine DNA methyltransferase / 0.666
4rto SFGDNA adenine methylase 2.1.1.72 0.666
4mb2 ATPUncharacterized protein / 0.665
4rtj SFGDNA adenine methylase 2.1.1.72 0.665
1mht SAHModification methylase HhaI 2.1.1.37 0.664
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.664
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.664
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.663
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.663
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.663
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.661
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.661
5epe SAHUncharacterized protein / 0.661
3wdm ADN4-phosphopantoate--beta-alanine ligase 6.3.2.36 0.660
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.659
3ou6 SAMSAM-dependent methyltransferase / 0.657
3p8z SAHGenome polyprotein 2.1.1.56 0.657
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.657
4rtq SAHDNA adenine methylase 2.1.1.72 0.656
8mht SAHModification methylase HhaI 2.1.1.37 0.656
2cdu ADPNADH oxidase / 0.655
2hmy SAMModification methylase HhaI 2.1.1.37 0.655
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.655
5bp7 SAHSAM-dependent methyltransferase / 0.654
4ctj SAMGenome polyprotein / 0.653
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.653
1fjx SAHModification methylase HhaI 2.1.1.37 0.652
3lcc SAHThiocyanate methyltransferase 1 / 0.652
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.652
1yf3 SAHDNA adenine methylase / 0.651
3kkz SAMUncharacterized protein / 0.651