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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
4rtk SAH DNA adenine methylase 2.1.1.72

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4rtk SAHDNA adenine methylase 2.1.1.72 0.984
2g1p SAHDNA adenine methylase 2.1.1.72 0.890
4rtm SAMDNA adenine methylase 2.1.1.72 0.885
4rtj SFGDNA adenine methylase 2.1.1.72 0.877
2ore SAHDNA adenine methylase 2.1.1.72 0.845
1yf3 SAHDNA adenine methylase / 0.842
4gbe SAHDNA adenine methylase 2.1.1.72 0.832
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.811
4rtq SAHDNA adenine methylase 2.1.1.72 0.807
4rto SFGDNA adenine methylase 2.1.1.72 0.802
1nw5 SAMModification methylase RsrI 2.1.1.72 0.795
1eg2 MTAModification methylase RsrI 2.1.1.72 0.791
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.786
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.780
4rtp SAMDNA adenine methylase 2.1.1.72 0.775
4rtr SAMDNA adenine methylase 2.1.1.72 0.767
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.761
4rts SAMDNA adenine methylase 2.1.1.72 0.759
1boo SAHModification methylase PvuII 2.1.1.113 0.751
3ldg SAHUncharacterized protein / 0.751
3tm5 SFGUncharacterized protein / 0.749
4rtn SAHDNA adenine methylase 2.1.1.72 0.744
4rtl SFGDNA adenine methylase 2.1.1.72 0.743
10mh SAHModification methylase HhaI 2.1.1.37 0.741
2uyh SAHModification methylase HhaI 2.1.1.37 0.741
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.741
4gol SA8DNA adenine methylase 2.1.1.72 0.737
3eey SAMrRNA methylase / 0.736
1skm SAHModification methylase HhaI 2.1.1.37 0.735
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.733
2c7q SAHModification methylase HhaI 2.1.1.37 0.731
3tm4 SAMUncharacterized protein / 0.731
1nw6 SFGModification methylase RsrI 2.1.1.72 0.730
5je4 SAHMethyl transferase / 0.727
2yxl SFG450aa long hypothetical fmu protein / 0.726
3go4 SAHUncharacterized protein / 0.726
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.726
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.726
3lcc SAHThiocyanate methyltransferase 1 / 0.725
5jdz SAHMethyl transferase / 0.725
1g60 SAMModification methylase MboII 2.1.1.72 0.722
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.722
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.720
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.720
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.720
4mht SAHModification methylase HhaI 2.1.1.37 0.718
5je3 SAHMethyl transferase / 0.718
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.715
2zif SAMMethyltransferase / 0.713
1uay ADNOxidoreductase / 0.711
3qv2 SAH5-cytosine DNA methyltransferase / 0.711
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.710
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.709
3tlj SAHUncharacterized protein / 0.708
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.707
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.707
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.707
2i9k SAHModification methylase HhaI 2.1.1.37 0.705
2hmv ADPKtr system potassium uptake protein A / 0.702
1mht SAHModification methylase HhaI 2.1.1.37 0.701
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.701
3m6v SAMRibosomal RNA small subunit methyltransferase F / 0.701
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.701
2px2 SAHGenome polyprotein 2.7.7.48 0.700
3mht SAHModification methylase HhaI 2.1.1.37 0.700
7mht SAHModification methylase HhaI 2.1.1.37 0.700
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.699
2zcj SAHModification methylase HhaI 2.1.1.37 0.698
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.698
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.697
4mb2 ATPUncharacterized protein / 0.697
8mht SAHModification methylase HhaI 2.1.1.37 0.697
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.695
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.695
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.693
4nec SAHPutative SAM-dependent methyltransferase / 0.693
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.692
4yv2 S4MSpermidine synthase, putative / 0.691
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.690
3cbg SAHO-methyltransferase / 0.690
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.690
3bwc SAMSpermidine synthase, putative / 0.688
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.686
4dmg SAMUncharacterized protein / 0.686
2z6u SAHModification methylase HhaI 2.1.1.37 0.685
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.685
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.684
2o06 MTASpermidine synthase 2.5.1.16 0.684
3ou2 SAHSAM-dependent methyltransferase / 0.684
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.683
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.683
2np7 NEAModification methylase TaqI 2.1.1.72 0.682
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.682
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.682
4uck SAMLarge structural protein / 0.682
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.682
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.681
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.679
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.678
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.678
9mht SAHModification methylase HhaI 2.1.1.37 0.678
3lkz SFGGenome polyprotein / 0.677
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.677
5mht SAHModification methylase HhaI 2.1.1.37 0.677
4ctk SAMGenome polyprotein / 0.676
4dkj SAHCytosine-specific methyltransferase / 0.676
1g1a NADdTDP-glucose 4,6-dehydratase / 0.675
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.675
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.675
2ibt NEAModification methylase TaqI 2.1.1.72 0.674
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.674
1af7 SAHChemotaxis protein methyltransferase 2.1.1.80 0.673
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.673
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.670
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.670
4kvz SAHPtnL protein / 0.670
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.669
5cku FADL-ornithine N(5)-monooxygenase / 0.669
3fpf MTAUncharacterized protein / 0.668
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.667
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.667
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.667
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.666
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.666
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.666
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.665
2p35 SAHTrans-aconitate 2-methyltransferase / 0.665
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.665
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.665
4kwc SAHMethyltransferase domain family / 0.664
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.664
1fjx SAHModification methylase HhaI 2.1.1.37 0.662
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.661
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.661
2f8l SAMLmo1582 protein / 0.660
3geg NADShort-chain dehydrogenase/reductase SDR / 0.660
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.660
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.659
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.658
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.657
4hh4 SAHCcbJ / 0.657
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.656
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.656
5jjr SAHGenome polyprotein / 0.656
2oy0 SAHGenome polyprotein / 0.655
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.655
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.655
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.654
2gsd NADFormate dehydrogenase / 0.654
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.654
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.653
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.652
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.652
3dzi RGTADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 3.2.2.6 0.650