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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
3emd SFG Methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3emd SFGMethyltransferase / 0.978
2px2 SAHGenome polyprotein 2.7.7.48 0.866
4k6m SAHGenome polyprotein / 0.845
3evb SAHGenome polyprotein 2.1.1.56 0.807
3ely SAHMethyltransferase / 0.806
2pxa SAHGenome polyprotein 2.7.7.48 0.803
3p97 SAMGenome polyprotein 2.1.1.56 0.802
4ctk SAMGenome polyprotein / 0.799
3eva SAHGenome polyprotein 2.1.1.56 0.791
3evc SAHGenome polyprotein 2.1.1.56 0.790
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.789
3p8z SAHGenome polyprotein 2.1.1.56 0.789
3eld SFGMethyltransferase / 0.788
2p41 SAHGenome polyprotein / 0.774
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.773
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.769
2px5 SAHGenome polyprotein 2.7.7.48 0.768
3lkz SFGGenome polyprotein / 0.766
4ctj SAMGenome polyprotein / 0.766
3c3y SAHO-methyltransferase / 0.765
2p3q SAHGenome polyprotein / 0.763
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.762
5jjr SAHGenome polyprotein / 0.756
3elu SAMMethyltransferase / 0.755
3p8z 36AGenome polyprotein 2.1.1.56 0.751
2plw SAMRibosomal RNA methyltransferase, putative / 0.747
2g1p SAHDNA adenine methylase 2.1.1.72 0.742
3evg SAHGenome polyprotein 2.1.1.56 0.742
2oy0 SAHGenome polyprotein / 0.733
3tos SAHCalS11 / 0.733
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.721
5dto SAHGenome polyprotein / 0.721
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.719
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.719
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.716
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.714
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.713
4uck SAMLarge structural protein / 0.713
2p1d SAHGenome polyprotein 2.7.7.48 0.711
2hnk SAHSAM-dependent O-methyltransferase / 0.708
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.705
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.700
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.700
5jjs SAHGenome polyprotein / 0.699
4gf5 SAHCalS11 / 0.698
1r6a SAHGenome polyprotein 2.7.7.48 0.696
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.689
1boo SAHModification methylase PvuII 2.1.1.113 0.688
2wa2 SAMGenome polyprotein / 0.685
2xbm SAHGenome polyprotein / 0.684
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.684
3tr6 SAHO-methyltransferase / 0.684
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.684
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.683
3cbg SAHO-methyltransferase / 0.682
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.679
5je2 SAHMethyl transferase / 0.679
10mh SAHModification methylase HhaI 2.1.1.37 0.674
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.674
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.670
7mht SAHModification methylase HhaI 2.1.1.37 0.670
1l9k SAHGenome polyprotein 2.7.7.48 0.668
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.668
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.668
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.668
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.667
2c7q SAHModification methylase HhaI 2.1.1.37 0.666
4c04 SFGProtein arginine N-methyltransferase 6 / 0.666
4rtj SFGDNA adenine methylase 2.1.1.72 0.666
4rtl SFGDNA adenine methylase 2.1.1.72 0.666
5jdz SAHMethyl transferase / 0.666
1skm SAHModification methylase HhaI 2.1.1.37 0.664
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.664
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.663
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.663
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.663
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.660
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.657
1mht SAHModification methylase HhaI 2.1.1.37 0.656
2z6u SAHModification methylase HhaI 2.1.1.37 0.656
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.656
3hvk 719Catechol O-methyltransferase 2.1.1.6 0.656
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.655
3iv6 SAMUncharacterized protein / 0.655
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.655
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.654
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.654
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.653
3nw9 637Catechol O-methyltransferase 2.1.1.6 0.653
4gbe SAHDNA adenine methylase 2.1.1.72 0.653
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.650
4oa5 SAHO-methyltransferase family protein / 0.650