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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
9mht SAH Modification methylase HhaI 2.1.1.37

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
9mht SAHModification methylase HhaI 2.1.1.37 0.984
10mh SAHModification methylase HhaI 2.1.1.37 0.929
5mht SAHModification methylase HhaI 2.1.1.37 0.919
2uyh SAHModification methylase HhaI 2.1.1.37 0.909
7mht SAHModification methylase HhaI 2.1.1.37 0.904
1skm SAHModification methylase HhaI 2.1.1.37 0.898
2c7q SAHModification methylase HhaI 2.1.1.37 0.891
8mht SAHModification methylase HhaI 2.1.1.37 0.866
2z6u SAHModification methylase HhaI 2.1.1.37 0.823
2zcj SAHModification methylase HhaI 2.1.1.37 0.788
4mht SAHModification methylase HhaI 2.1.1.37 0.778
3qv2 SAH5-cytosine DNA methyltransferase / 0.774
2i9k SAHModification methylase HhaI 2.1.1.37 0.771
3mht SAHModification methylase HhaI 2.1.1.37 0.763
2hmy SAMModification methylase HhaI 2.1.1.37 0.749
1mht SAHModification methylase HhaI 2.1.1.37 0.748
3tm4 SAMUncharacterized protein / 0.745
2px2 SAHGenome polyprotein 2.7.7.48 0.726
4dkj SAHCytosine-specific methyltransferase / 0.721
3ou2 SAHSAM-dependent methyltransferase / 0.714
3cbg SAHO-methyltransferase / 0.713
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.704
2cww SAHUncharacterized protein / 0.703
3c3y SAHO-methyltransferase / 0.700
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.700
2pxa SAHGenome polyprotein 2.7.7.48 0.698
4nec SAHPutative SAM-dependent methyltransferase / 0.698
2br5 SAHCephalosporin hydroxylase CmcI / 0.697
4mb2 ATPUncharacterized protein / 0.697
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.696
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.696
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.695
4rtj SFGDNA adenine methylase 2.1.1.72 0.695
1g60 SAMModification methylase MboII 2.1.1.72 0.694
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.693
2g1p SAHDNA adenine methylase 2.1.1.72 0.692
2f8l SAMLmo1582 protein / 0.691
4rtl SFGDNA adenine methylase 2.1.1.72 0.688
4uck SAMLarge structural protein / 0.688
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.687
5bxy SAHPutative RNA methylase family UPF0020 / 0.686
1nw5 SAMModification methylase RsrI 2.1.1.72 0.685
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.685
1fjx SAHModification methylase HhaI 2.1.1.37 0.684
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.684
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.681
4k6m SAHGenome polyprotein / 0.681
4rtm SAMDNA adenine methylase 2.1.1.72 0.681
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.679
4rtk SAHDNA adenine methylase 2.1.1.72 0.678
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.677
2np7 NEAModification methylase TaqI 2.1.1.72 0.677
2p35 SAHTrans-aconitate 2-methyltransferase / 0.676
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.676
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.675
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.675
2zif SAMMethyltransferase / 0.675
3p8z SAHGenome polyprotein 2.1.1.56 0.674
4ctj SAMGenome polyprotein / 0.674
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.674
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.673
5bp9 SAHPutative methyltransferase protein / 0.672
1nw6 SFGModification methylase RsrI 2.1.1.72 0.671
2ore SAHDNA adenine methylase 2.1.1.72 0.670
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.669
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.669
1nhs FADNADH peroxidase 1.11.1.1 0.668
3tm5 SFGUncharacterized protein / 0.668
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.667
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.667
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.666
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.665
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.665
3ldg SAHUncharacterized protein / 0.664
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.664
4ctk SAMGenome polyprotein / 0.663
4tm4 FDAKtzI / 0.663
1npx FADNADH peroxidase 1.11.1.1 0.662
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.662
3hvk 719Catechol O-methyltransferase 2.1.1.6 0.662
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.662
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.662
4tlx FDAKtzI / 0.662
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.662
2ih5 NEAModification methylase TaqI 2.1.1.72 0.661
2o06 MTASpermidine synthase 2.5.1.16 0.661
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.661
3tos SAHCalS11 / 0.661
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.661
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.660
3nlc FADUncharacterized protein / 0.660
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.660
4eqr FADCoenzyme A disulfide reductase / 0.660
4eqs FADCoenzyme A disulfide reductase / 0.660
4eqw FADCoenzyme A disulfide reductase / 0.660
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.660
1n4v FADCholesterol oxidase 1.1.3.6 0.659
4rto SFGDNA adenine methylase 2.1.1.72 0.659
4yuz S4MSpermidine synthase, putative / 0.659
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.658
3ntd FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.658
3tlj SAHUncharacterized protein / 0.658
4ysh FADGlycine oxidase / 0.658
1f3l SAHProtein arginine N-methyltransferase 3 / 0.657
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.657
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.657
4g6h NAIRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial 1.6.5.9 0.657
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.656
1v59 NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.656
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.656
2yqz SAMUncharacterized protein / 0.656
3n1s 5GPPurine nucleoside phosphoramidase / 0.656
1eg2 MTAModification methylase RsrI 2.1.1.72 0.655
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.655
2qa2 FADPolyketide oxygenase CabE / 0.655
3eey SAMrRNA methylase / 0.655
3lst SAHCalO1 / 0.655
4c03 SFGProtein arginine N-methyltransferase 6 / 0.655
4c04 SFGProtein arginine N-methyltransferase 6 / 0.655
4poo SAMPutative RNA methylase / 0.655
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.655
1nhp FADNADH peroxidase 1.11.1.1 0.654
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.654
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.654
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.653
4rtr SAMDNA adenine methylase 2.1.1.72 0.653
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.652
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.652
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.652
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.652
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.652
1cbo FADCholesterol oxidase 1.1.3.6 0.651
2wa2 SAMGenome polyprotein / 0.651
3eva SAHGenome polyprotein 2.1.1.56 0.651
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.651
4nzh FADL-ornithine N(5)-monooxygenase / 0.651
4rek FADCholesterol oxidase 1.1.3.6 0.651
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.650
1mxt FAECholesterol oxidase 1.1.3.6 0.650
1n1p FADCholesterol oxidase 1.1.3.6 0.650
1n4w FADCholesterol oxidase 1.1.3.6 0.650
2hmv ADPKtr system potassium uptake protein A / 0.650
2px5 SAHGenome polyprotein 2.7.7.48 0.650
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.650
4xwr FADCholesterol oxidase 1.1.3.6 0.650
4xxg FADCholesterol oxidase 1.1.3.6 0.650