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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
2dpm SAM Modification methylase DpnIIA 2.1.1.72

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.985
2g1p SAHDNA adenine methylase 2.1.1.72 0.911
4rtk SAHDNA adenine methylase 2.1.1.72 0.811
1yf3 SAHDNA adenine methylase / 0.800
4gbe SAHDNA adenine methylase 2.1.1.72 0.785
4rtj SFGDNA adenine methylase 2.1.1.72 0.784
2ore SAHDNA adenine methylase 2.1.1.72 0.770
4rtl SFGDNA adenine methylase 2.1.1.72 0.769
4rtm SAMDNA adenine methylase 2.1.1.72 0.765
1eg2 MTAModification methylase RsrI 2.1.1.72 0.764
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.758
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.756
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.756
1g60 SAMModification methylase MboII 2.1.1.72 0.752
4rtq SAHDNA adenine methylase 2.1.1.72 0.746
1boo SAHModification methylase PvuII 2.1.1.113 0.745
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.744
3tm4 SAMUncharacterized protein / 0.743
1nw5 SAMModification methylase RsrI 2.1.1.72 0.742
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.740
2cww SAHUncharacterized protein / 0.739
4rto SFGDNA adenine methylase 2.1.1.72 0.739
3ldg SAHUncharacterized protein / 0.737
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.728
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.727
2yxl SFG450aa long hypothetical fmu protein / 0.727
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.726
2px2 SAHGenome polyprotein 2.7.7.48 0.724
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.723
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.722
1skm SAHModification methylase HhaI 2.1.1.37 0.719
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.714
1nw6 SFGModification methylase RsrI 2.1.1.72 0.713
4gol SA8DNA adenine methylase 2.1.1.72 0.713
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.712
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.712
3m6v SAMRibosomal RNA small subunit methyltransferase F / 0.711
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.710
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.709
4rts SAMDNA adenine methylase 2.1.1.72 0.708
4rtn SAHDNA adenine methylase 2.1.1.72 0.707
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.704
9mht SAHModification methylase HhaI 2.1.1.37 0.704
2z6u SAHModification methylase HhaI 2.1.1.37 0.703
4rtp SAMDNA adenine methylase 2.1.1.72 0.703
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.701
4rtr SAMDNA adenine methylase 2.1.1.72 0.701
1y9d FADPyruvate oxidase 1.2.3.3 0.700
3tm5 SFGUncharacterized protein / 0.700
1r6a SAHGenome polyprotein 2.7.7.48 0.698
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.697
10mh SAHModification methylase HhaI 2.1.1.37 0.696
3ldf SAHUncharacterized protein / 0.696
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.695
8mht SAHModification methylase HhaI 2.1.1.37 0.695
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.693
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.692
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.692
4uck SAMLarge structural protein / 0.692
4mb2 ATPUncharacterized protein / 0.690
3tr6 SAHO-methyltransferase / 0.689
5mht SAHModification methylase HhaI 2.1.1.37 0.688
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.686
3p8z SAHGenome polyprotein 2.1.1.56 0.685
2c7q SAHModification methylase HhaI 2.1.1.37 0.683
2hmv ADPKtr system potassium uptake protein A / 0.682
2i9k SAHModification methylase HhaI 2.1.1.37 0.682
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.682
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.681
2uyh SAHModification methylase HhaI 2.1.1.37 0.680
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.680
1v5e FADPyruvate oxidase / 0.679
3mht SAHModification methylase HhaI 2.1.1.37 0.679
3tlj SAHUncharacterized protein / 0.679
4dmg SAMUncharacterized protein / 0.679
2px5 SAHGenome polyprotein 2.7.7.48 0.678
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.677
3eva SAHGenome polyprotein 2.1.1.56 0.676
3lkz SFGGenome polyprotein / 0.676
1uay ADNOxidoreductase / 0.675
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.675
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.674
4k6m SAHGenome polyprotein / 0.674
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.673
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.673
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.673
2ih2 NEAModification methylase TaqI 2.1.1.72 0.672
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.672
7mht SAHModification methylase HhaI 2.1.1.37 0.672
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.671
3wdm ADN4-phosphopantoate--beta-alanine ligase 6.3.2.36 0.670
2ih5 NEAModification methylase TaqI 2.1.1.72 0.669
2p41 SAHGenome polyprotein / 0.669
2zcj SAHModification methylase HhaI 2.1.1.37 0.669
4dkj SAHCytosine-specific methyltransferase / 0.669
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.669
2pxa SAHGenome polyprotein 2.7.7.48 0.668
2zif SAMMethyltransferase / 0.667
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.666
3elu SAMMethyltransferase / 0.666
4poo SAMPutative RNA methylase / 0.665
3emd SFGMethyltransferase / 0.664
4ctj SAMGenome polyprotein / 0.663
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.663
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.662
1aqi SAHModification methylase TaqI 2.1.1.72 0.662
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.662
2dji FADPyruvate oxidase / 0.662
4ctk SAMGenome polyprotein / 0.661
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.661
2np6 NEAModification methylase TaqI 2.1.1.72 0.660
3go4 SAHUncharacterized protein / 0.660
2yy7 NADL-threonine dehydrogenase / 0.659
3c3y SAHO-methyltransferase / 0.659
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.659
3p97 SAMGenome polyprotein 2.1.1.56 0.658
3ikt NADRedox-sensing transcriptional repressor Rex / 0.657
4mht SAHModification methylase HhaI 2.1.1.37 0.657
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.656
3eld SFGMethyltransferase / 0.656
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.656
3qv2 SAH5-cytosine DNA methyltransferase / 0.655
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.655
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.654
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.654
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.654
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.654
3adp NAILambda-crystallin 1.1.1.45 0.653
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.653
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.653
4kvz SAHPtnL protein / 0.653
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.652
3lcc SAHThiocyanate methyltransferase 1 / 0.652
5jjr SAHGenome polyprotein / 0.651
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.650
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.650
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.650