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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
2yxl SFG 450aa long hypothetical fmu protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2yxl SFG450aa long hypothetical fmu protein / 1.045
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.889
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.882
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.812
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.795
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.792
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.784
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.784
3ldf SAHUncharacterized protein / 0.770
3m6w SAMRibosomal RNA small subunit methyltransferase F / 0.769
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.768
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.766
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.766
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.762
2g1p SAHDNA adenine methylase 2.1.1.72 0.761
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.753
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.746
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.746
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.739
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.737
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.736
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.735
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.735
4gbe SAHDNA adenine methylase 2.1.1.72 0.734
2ore SAHDNA adenine methylase 2.1.1.72 0.732
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.729
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.729
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.727
4rtk SAHDNA adenine methylase 2.1.1.72 0.726
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.724
3ou6 SAMSAM-dependent methyltransferase / 0.724
4mb2 ATPUncharacterized protein / 0.722
5je3 SAHMethyl transferase / 0.721
3cbg SAHO-methyltransferase / 0.716
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.714
1skm SAHModification methylase HhaI 2.1.1.37 0.713
2i9k SAHModification methylase HhaI 2.1.1.37 0.712
2z6u SAHModification methylase HhaI 2.1.1.37 0.712
2c7q SAHModification methylase HhaI 2.1.1.37 0.711
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.711
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.710
5je4 SAHMethyl transferase / 0.709
1boo SAHModification methylase PvuII 2.1.1.113 0.705
2f8l SAMLmo1582 protein / 0.703
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.703
1nw5 SAMModification methylase RsrI 2.1.1.72 0.702
3ldg SAHUncharacterized protein / 0.702
1eg2 MTAModification methylase RsrI 2.1.1.72 0.701
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.701
2px2 SAHGenome polyprotein 2.7.7.48 0.700
3mht SAHModification methylase HhaI 2.1.1.37 0.700
4dmg SAMUncharacterized protein / 0.700
4rtj SFGDNA adenine methylase 2.1.1.72 0.700
2ih2 NEAModification methylase TaqI 2.1.1.72 0.698
2zcj SAHModification methylase HhaI 2.1.1.37 0.698
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.697
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.695
2plw SAMRibosomal RNA methyltransferase, putative / 0.695
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.695
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.695
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.695
4oa5 SAHO-methyltransferase family protein / 0.693
3m6v SAMRibosomal RNA small subunit methyltransferase F / 0.692
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.690
3eld SFGMethyltransferase / 0.690
4rtm SAMDNA adenine methylase 2.1.1.72 0.689
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.687
4rts SAMDNA adenine methylase 2.1.1.72 0.687
1fjx SAHModification methylase HhaI 2.1.1.37 0.686
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.686
2px5 SAHGenome polyprotein 2.7.7.48 0.686
4ctk SAMGenome polyprotein / 0.686
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.684
4rtq SAHDNA adenine methylase 2.1.1.72 0.684
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.684
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.683
4rtr SAMDNA adenine methylase 2.1.1.72 0.682
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.681
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.680
4yv2 S4MSpermidine synthase, putative / 0.678
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.678
3tm4 SAMUncharacterized protein / 0.677
3p8z SAHGenome polyprotein 2.1.1.56 0.676
1y9d FADPyruvate oxidase 1.2.3.3 0.675
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.675
4ctj SAMGenome polyprotein / 0.675
2zif SAMMethyltransferase / 0.674
4yuz S4MSpermidine synthase, putative / 0.674
3eey SAMrRNA methylase / 0.673
4dkj SAHCytosine-specific methyltransferase / 0.673
7mht SAHModification methylase HhaI 2.1.1.37 0.673
1yf3 SAHDNA adenine methylase / 0.672
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.672
4rto SFGDNA adenine methylase 2.1.1.72 0.672
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.671
4lwp SAHArginine N-methyltransferase, putative / 0.671
2cww SAHUncharacterized protein / 0.670
3tos SAHCalS11 / 0.670
4tm4 FDAKtzI / 0.670
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.670
2p35 SAHTrans-aconitate 2-methyltransferase / 0.669
3c3y SAHO-methyltransferase / 0.669
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.668
1aqi SAHModification methylase TaqI 2.1.1.72 0.667
3evc SAHGenome polyprotein 2.1.1.56 0.667
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.666
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.665
1v5e FADPyruvate oxidase / 0.665
3tm5 SFGUncharacterized protein / 0.665
1pow FADPyruvate oxidase 1.2.3.3 0.664
4mht SAHModification methylase HhaI 2.1.1.37 0.664
2dji FADPyruvate oxidase / 0.663
2yqz SAMUncharacterized protein / 0.663
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.663
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.663
3eva SAHGenome polyprotein 2.1.1.56 0.662
3ou2 SAHSAM-dependent methyltransferase / 0.662
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.662
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.662
1f3l SAHProtein arginine N-methyltransferase 3 / 0.661
2wa2 SAMGenome polyprotein / 0.660
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.660
3p97 SAMGenome polyprotein 2.1.1.56 0.660
4rtl SFGDNA adenine methylase 2.1.1.72 0.660
2uyh SAHModification methylase HhaI 2.1.1.37 0.659
4tlx FDAKtzI / 0.659
5je2 SAHMethyl transferase / 0.659
1joa FADNADH peroxidase 1.11.1.1 0.658
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.658
3abi NADUncharacterized protein / 0.658
5jjr SAHGenome polyprotein / 0.658
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.657
2np7 NEAModification methylase TaqI 2.1.1.72 0.657
2rgj FADFlavin-containing monooxygenase / 0.657
3lkz SFGGenome polyprotein / 0.657
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.657
10mh SAHModification methylase HhaI 2.1.1.37 0.656
3tlj SAHUncharacterized protein / 0.656
4hb9 FADUncharacterized protein / 0.656
4wec NADShort chain dehydrogenase / 0.656
1cbo FADCholesterol oxidase 1.1.3.6 0.655
3alm FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.655
3elu SAMMethyltransferase / 0.655
4emw FADCoenzyme A disulfide reductase / 0.655
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.654
2np6 NEAModification methylase TaqI 2.1.1.72 0.654
3ea4 FABAcetolactate synthase, chloroplastic 2.2.1.6 0.654
3ely SAHMethyltransferase / 0.654
3rw9 DSHSpermidine synthase 2.5.1.16 0.654
4eqx FADCoenzyme A disulfide reductase / 0.654
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.653
2wzb ADPPhosphoglycerate kinase 1 2.7.2.3 0.653
3nta FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.653
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.653
4tlz FADKtzI / 0.653
4u2t FADCholesterol oxidase 1.1.3.6 0.653
2oy0 SAHGenome polyprotein / 0.652
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.652
4uck SAMLarge structural protein / 0.652
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.651
1zmc FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.651
2ibt NEAModification methylase TaqI 2.1.1.72 0.651
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.651
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.651
1g38 NEAModification methylase TaqI 2.1.1.72 0.650
1ijh FADCholesterol oxidase 1.1.3.6 0.650
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.650
4mo2 FDAUDP-galactopyranose mutase / 0.650