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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
2px2 SAH Genome polyprotein 2.7.7.48

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2px2 SAHGenome polyprotein 2.7.7.48 0.953
3emd SFGMethyltransferase / 0.866
4k6m SAHGenome polyprotein / 0.846
4ctk SAMGenome polyprotein / 0.836
3lkz SFGGenome polyprotein / 0.835
3evc SAHGenome polyprotein 2.1.1.56 0.834
5jjr SAHGenome polyprotein / 0.825
3p8z SAHGenome polyprotein 2.1.1.56 0.824
4ctj SAMGenome polyprotein / 0.821
3p97 SAMGenome polyprotein 2.1.1.56 0.814
3evb SAHGenome polyprotein 2.1.1.56 0.802
2g1p SAHDNA adenine methylase 2.1.1.72 0.794
2px5 SAHGenome polyprotein 2.7.7.48 0.793
3eld SFGMethyltransferase / 0.792
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.786
2pxa SAHGenome polyprotein 2.7.7.48 0.785
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.783
3eva SAHGenome polyprotein 2.1.1.56 0.783
2plw SAMRibosomal RNA methyltransferase, putative / 0.777
3ely SAHMethyltransferase / 0.777
3p8z 36AGenome polyprotein 2.1.1.56 0.767
2p3q SAHGenome polyprotein / 0.765
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.754
2oy0 SAHGenome polyprotein / 0.753
3elu SAMMethyltransferase / 0.750
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.746
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.746
1r6a SAHGenome polyprotein 2.7.7.48 0.743
2wa2 SAMGenome polyprotein / 0.742
5dto SAHGenome polyprotein / 0.741
1yf3 SAHDNA adenine methylase / 0.737
2p41 SAHGenome polyprotein / 0.727
4rtj SFGDNA adenine methylase 2.1.1.72 0.727
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.726
9mht SAHModification methylase HhaI 2.1.1.37 0.726
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.724
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.724
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.717
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.715
2p1d SAHGenome polyprotein 2.7.7.48 0.713
2hnk SAHSAM-dependent O-methyltransferase / 0.711
4uck SAMLarge structural protein / 0.708
3evg SAHGenome polyprotein 2.1.1.56 0.704
5jjs SAHGenome polyprotein / 0.703
7mht SAHModification methylase HhaI 2.1.1.37 0.701
2yxl SFG450aa long hypothetical fmu protein / 0.700
4rtk SAHDNA adenine methylase 2.1.1.72 0.700
3c3y SAHO-methyltransferase / 0.698
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.698
1l9k SAHGenome polyprotein 2.7.7.48 0.697
10mh SAHModification methylase HhaI 2.1.1.37 0.695
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.695
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.693
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.692
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.691
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.690
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.687
1boo SAHModification methylase PvuII 2.1.1.113 0.686
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.684
2zif SAMMethyltransferase / 0.681
4gbe SAHDNA adenine methylase 2.1.1.72 0.680
4oa5 SAHO-methyltransferase family protein / 0.680
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.680
3tm4 SAMUncharacterized protein / 0.679
4gf5 SAHCalS11 / 0.678
2zcj SAHModification methylase HhaI 2.1.1.37 0.677
1skm SAHModification methylase HhaI 2.1.1.37 0.676
2np7 NEAModification methylase TaqI 2.1.1.72 0.675
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.675
2z6u SAHModification methylase HhaI 2.1.1.37 0.673
5je4 SAHMethyl transferase / 0.672
1nw5 SAMModification methylase RsrI 2.1.1.72 0.671
2i9k SAHModification methylase HhaI 2.1.1.37 0.671
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.671
8mht SAHModification methylase HhaI 2.1.1.37 0.671
2uyh SAHModification methylase HhaI 2.1.1.37 0.669
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.669
2cww SAHUncharacterized protein / 0.668
3ou2 SAHSAM-dependent methyltransferase / 0.668
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.668
2xbm SAHGenome polyprotein / 0.667
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.667
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.666
3cbg SAHO-methyltransferase / 0.666
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.664
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.664
4rtl SFGDNA adenine methylase 2.1.1.72 0.663
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.663
1fjx SAHModification methylase HhaI 2.1.1.37 0.662
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.662
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.662
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.662
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.661
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.661
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.660
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.660
1mht SAHModification methylase HhaI 2.1.1.37 0.658
2c7q SAHModification methylase HhaI 2.1.1.37 0.658
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.658
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.656
2o06 MTASpermidine synthase 2.5.1.16 0.656
3fpf MTAUncharacterized protein / 0.656
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.656
3tr6 SAHO-methyltransferase / 0.656
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.656
5je3 SAHMethyl transferase / 0.656
1g60 SAMModification methylase MboII 2.1.1.72 0.654
1n4v FADCholesterol oxidase 1.1.3.6 0.653
2o07 MTASpermidine synthase 2.5.1.16 0.653
4rek FADCholesterol oxidase 1.1.3.6 0.653
5jdz SAHMethyl transferase / 0.653
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.652
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.652
1ve3 SAMUncharacterized protein / 0.651
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.651
4c04 SFGProtein arginine N-methyltransferase 6 / 0.651
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.650