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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
2px5 SAH Genome polyprotein 2.7.7.48

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2px5 SAHGenome polyprotein 2.7.7.48 0.912
3p97 SAMGenome polyprotein 2.1.1.56 0.819
5jjr SAHGenome polyprotein / 0.798
4ctj SAMGenome polyprotein / 0.795
2px2 SAHGenome polyprotein 2.7.7.48 0.793
1r6a SAHGenome polyprotein 2.7.7.48 0.788
3evc SAHGenome polyprotein 2.1.1.56 0.788
3eva SAHGenome polyprotein 2.1.1.56 0.787
3p8z SAHGenome polyprotein 2.1.1.56 0.785
4ctk SAMGenome polyprotein / 0.780
2p41 SAHGenome polyprotein / 0.772
3evb SAHGenome polyprotein 2.1.1.56 0.771
3eld SFGMethyltransferase / 0.770
3elu SAMMethyltransferase / 0.768
3emd SFGMethyltransferase / 0.768
1l9k SAHGenome polyprotein 2.7.7.48 0.760
3lkz SFGGenome polyprotein / 0.754
2pxa SAHGenome polyprotein 2.7.7.48 0.753
4k6m SAHGenome polyprotein / 0.747
3ely SAHMethyltransferase / 0.744
3p8z 36AGenome polyprotein 2.1.1.56 0.744
3evg SAHGenome polyprotein 2.1.1.56 0.738
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.734
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.734
1yf3 SAHDNA adenine methylase / 0.732
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.731
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.731
2p3q SAHGenome polyprotein / 0.726
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.724
2wa2 SAMGenome polyprotein / 0.722
5dto SAHGenome polyprotein / 0.714
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.708
2p1d SAHGenome polyprotein 2.7.7.48 0.706
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.706
3c3y SAHO-methyltransferase / 0.705
2g1p SAHDNA adenine methylase 2.1.1.72 0.703
3tos SAHCalS11 / 0.699
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.697
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.695
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.693
4gf5 SAHCalS11 / 0.691
2plw SAMRibosomal RNA methyltransferase, putative / 0.689
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.686
2yxl SFG450aa long hypothetical fmu protein / 0.686
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.683
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.679
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.678
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.677
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.675
4uck SAMLarge structural protein / 0.674
5jjs SAHGenome polyprotein / 0.673
1skm SAHModification methylase HhaI 2.1.1.37 0.670
2c7q SAHModification methylase HhaI 2.1.1.37 0.669
3mht SAHModification methylase HhaI 2.1.1.37 0.669
1boo SAHModification methylase PvuII 2.1.1.113 0.668
2xbm SAHGenome polyprotein / 0.668
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.667
2uyh SAHModification methylase HhaI 2.1.1.37 0.666
10mh SAHModification methylase HhaI 2.1.1.37 0.665
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.665
2hnk SAHSAM-dependent O-methyltransferase / 0.664
1fjx SAHModification methylase HhaI 2.1.1.37 0.663
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.663
1mht SAHModification methylase HhaI 2.1.1.37 0.661
2i9k SAHModification methylase HhaI 2.1.1.37 0.661
4dmg SAMUncharacterized protein / 0.657
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.657
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.656
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.656
4rtl SFGDNA adenine methylase 2.1.1.72 0.656
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.655
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.654
2oy0 SAHGenome polyprotein / 0.653
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.653
7mht SAHModification methylase HhaI 2.1.1.37 0.653
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.652
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.651
3vyw SAMUncharacterized protein / 0.650
9mht SAHModification methylase HhaI 2.1.1.37 0.650