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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
2xyr SFG Replicase polyprotein 1ab 2.1.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2xyr SFGReplicase polyprotein 1ab 2.1.1 1.006
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.732
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.731
4dmg SAMUncharacterized protein / 0.719
2hnk SAHSAM-dependent O-methyltransferase / 0.715
3cbg SAHO-methyltransferase / 0.707
3wv8 ATPHmd co-occurring protein HcgE / 0.705
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.705
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.701
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.700
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.698
3tos SAHCalS11 / 0.698
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.691
2plw SAMRibosomal RNA methyltransferase, putative / 0.689
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.689
3wv7 ADPHmd co-occurring protein HcgE / 0.684
4yuv S4MSpermidine synthase, putative / 0.682
1ptj SNDNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.681
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.680
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.678
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.678
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.678
3ldf SAHUncharacterized protein / 0.676
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.675
5je4 SAHMethyl transferase / 0.673
4k6m SAHGenome polyprotein / 0.671
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.670
2z6u SAHModification methylase HhaI 2.1.1.37 0.668
2zcj SAHModification methylase HhaI 2.1.1.37 0.668
3bwc SAMSpermidine synthase, putative / 0.667
3go4 SAHUncharacterized protein / 0.667
1g1a NADdTDP-glucose 4,6-dehydratase / 0.666
4yuz S4MSpermidine synthase, putative / 0.666
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.666
3m6w SAMRibosomal RNA small subunit methyltransferase F / 0.664
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.664
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.663
2yqz SAMUncharacterized protein / 0.663
3emd SFGMethyltransferase / 0.663
3ldg SAHUncharacterized protein / 0.663
7mht SAHModification methylase HhaI 2.1.1.37 0.662
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.661
3duw SAHO-methyltransferase, putative / 0.661
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.661
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.660
2p35 SAHTrans-aconitate 2-methyltransferase / 0.660
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.658
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.658
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.658
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.658
1nw5 SAMModification methylase RsrI 2.1.1.72 0.657
2i9k SAHModification methylase HhaI 2.1.1.37 0.657
3ou6 SAMSAM-dependent methyltransferase / 0.657
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.657
1ori SAHProtein arginine N-methyltransferase 1 / 0.656
4c04 SFGProtein arginine N-methyltransferase 6 / 0.656
5bxy SAHPutative RNA methylase family UPF0020 / 0.656
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.654
3ou2 SAHSAM-dependent methyltransferase / 0.654
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.654
4lwp SAHArginine N-methyltransferase, putative / 0.654
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.653
2oy0 SAHGenome polyprotein / 0.652
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.652
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.652
4yv2 S4MSpermidine synthase, putative / 0.652
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.651
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.650