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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
4ctk SAM Genome polyprotein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4ctk SAMGenome polyprotein / 0.880
5jjr SAHGenome polyprotein / 0.859
2px2 SAHGenome polyprotein 2.7.7.48 0.836
3lkz SFGGenome polyprotein / 0.817
3p8z SAHGenome polyprotein 2.1.1.56 0.814
4ctj SAMGenome polyprotein / 0.814
3eld SFGMethyltransferase / 0.807
3p8z 36AGenome polyprotein 2.1.1.56 0.802
3emd SFGMethyltransferase / 0.799
3evb SAHGenome polyprotein 2.1.1.56 0.790
4k6m SAHGenome polyprotein / 0.790
3eva SAHGenome polyprotein 2.1.1.56 0.785
3p97 SAMGenome polyprotein 2.1.1.56 0.784
2px5 SAHGenome polyprotein 2.7.7.48 0.780
2p41 SAHGenome polyprotein / 0.770
3evc SAHGenome polyprotein 2.1.1.56 0.770
2pxa SAHGenome polyprotein 2.7.7.48 0.761
5dto SAHGenome polyprotein / 0.760
3elu SAMMethyltransferase / 0.759
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.754
3ely SAHMethyltransferase / 0.746
2g1p SAHDNA adenine methylase 2.1.1.72 0.742
1r6a SAHGenome polyprotein 2.7.7.48 0.738
2p3q SAHGenome polyprotein / 0.736
3tos SAHCalS11 / 0.730
2hnk SAHSAM-dependent O-methyltransferase / 0.726
2oy0 SAHGenome polyprotein / 0.725
3c3y SAHO-methyltransferase / 0.725
5jjs SAHGenome polyprotein / 0.724
1l9k SAHGenome polyprotein 2.7.7.48 0.720
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.713
1yf3 SAHDNA adenine methylase / 0.712
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.712
2wa2 SAMGenome polyprotein / 0.711
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.711
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.710
2p1d SAHGenome polyprotein 2.7.7.48 0.709
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.709
4gf5 SAHCalS11 / 0.705
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.703
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.702
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.702
2plw SAMRibosomal RNA methyltransferase, putative / 0.699
4uck SAMLarge structural protein / 0.696
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.692
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.692
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.692
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.689
3evg SAHGenome polyprotein 2.1.1.56 0.688
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.688
2yxl SFG450aa long hypothetical fmu protein / 0.686
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.685
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.679
3cbg SAHO-methyltransferase / 0.677
4rtk SAHDNA adenine methylase 2.1.1.72 0.676
2i9k SAHModification methylase HhaI 2.1.1.37 0.675
2xbm SAHGenome polyprotein / 0.673
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.673
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.673
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.672
1skm SAHModification methylase HhaI 2.1.1.37 0.671
2c7q SAHModification methylase HhaI 2.1.1.37 0.670
3mht SAHModification methylase HhaI 2.1.1.37 0.669
1mht SAHModification methylase HhaI 2.1.1.37 0.666
4gbe SAHDNA adenine methylase 2.1.1.72 0.664
9mht SAHModification methylase HhaI 2.1.1.37 0.663
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.662
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.661
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.661
3vyw SAMUncharacterized protein / 0.660
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.657
4dmg SAMUncharacterized protein / 0.657
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.655
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.655
5jdz SAHMethyl transferase / 0.655
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.654
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.654
7mht SAHModification methylase HhaI 2.1.1.37 0.654
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.653
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.653
1boo SAHModification methylase PvuII 2.1.1.113 0.652
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.652
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.652
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.650
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.650