sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.941 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.911 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.904 | |
| 5mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.890 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.888 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.886 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.872 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.872 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.851 | |
| 8mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.850 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.849 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.830 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.816 | |
| 4mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.791 | |
| 1fjx | SAH | Modification methylase HhaI | 2.1.1.37 | 0.784 | |
| 4dkj | SAH | Cytosine-specific methyltransferase | / | 0.784 | |
| 3qv2 | SAH | 5-cytosine DNA methyltransferase | / | 0.753 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.752 | |
| 2hmy | SAM | Modification methylase HhaI | 2.1.1.37 | 0.746 | |
| 2zif | SAM | Methyltransferase | / | 0.735 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.730 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.721 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.719 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.719 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.718 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.718 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.718 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.718 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.718 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.714 | |
| 2f8l | SAM | Lmo1582 protein | / | 0.714 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.714 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.711 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.711 | |
| 3eey | SAM | rRNA methylase | / | 0.709 | |
| 4hh4 | SAH | CcbJ | / | 0.708 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.708 | |
| 3c3y | SAH | O-methyltransferase | / | 0.707 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.707 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.706 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.706 | |
| 2np6 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.705 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.705 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.704 | |
| 4h0n | SAH | Dnmt2 | / | 0.704 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.703 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.703 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.702 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.702 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.701 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.701 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.701 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.700 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.700 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.700 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.698 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.697 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.697 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.697 | |
| 4poo | SAM | Putative RNA methylase | / | 0.697 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.697 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.696 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.695 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.695 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.695 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.694 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.694 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.693 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.693 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.692 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.692 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.692 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.691 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.691 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.691 | |
| 3swr | SFG | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.690 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.689 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.689 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.687 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.686 | |
| 2br5 | SAH | Cephalosporin hydroxylase CmcI | / | 0.685 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.685 | |
| 3cbg | SAH | O-methyltransferase | / | 0.685 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.685 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.685 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.685 | |
| 4egu | 5GP | Putative histidine triad (HIT) protein | / | 0.684 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.681 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.681 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.681 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.680 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.680 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.680 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.680 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.680 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.679 | |
| 3tlj | SAH | Uncharacterized protein | / | 0.679 | |
| 4rtl | SFG | DNA adenine methylase | 2.1.1.72 | 0.679 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.678 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.678 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.678 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.677 | |
| 2pxa | SAH | Genome polyprotein | 2.7.7.48 | 0.677 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.677 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.677 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.676 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.676 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.675 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.674 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.674 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.674 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.674 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.674 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.673 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.673 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.673 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.673 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.673 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.672 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.672 | |
| 4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.672 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.672 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.672 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.671 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.671 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.671 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.671 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.671 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.671 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.671 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.670 | |
| 3emd | SFG | Methyltransferase | / | 0.670 | |
| 4rtq | SAH | DNA adenine methylase | 2.1.1.72 | 0.670 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.669 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.668 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.667 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.666 | |
| 3ou7 | SAM | SAM-dependent methyltransferase | / | 0.666 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.665 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.665 | |
| 2ixa | NAD | Alpha-N-acetylgalactosaminidase | 3.2.1.49 | 0.665 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.664 | |
| 3lhd | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.664 | |
| 3pt6 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.664 | |
| 4tm4 | FDA | KtzI | / | 0.664 | |
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.663 | |
| 1v59 | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.663 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.663 | |
| 2hms | NAI | Ktr system potassium uptake protein A | / | 0.663 | |
| 3hvk | 719 | Catechol O-methyltransferase | 2.1.1.6 | 0.663 | |
| 3n1s | 5GP | Purine nucleoside phosphoramidase | / | 0.663 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.663 | |
| 2xyr | SFG | Replicase polyprotein 1ab | 2.1.1 | 0.662 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.662 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.662 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.662 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.662 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.661 | |
| 2dki | FAD | 3-hydroxybenzoate 4-monooxygenase | 1.14.13.23 | 0.661 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.661 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.661 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.660 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.660 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.660 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.660 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.660 | |
| 4rto | SFG | DNA adenine methylase | 2.1.1.72 | 0.660 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.660 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.660 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 3gyj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 3p8z | SAH | Genome polyprotein | 2.1.1.56 | 0.659 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.659 | |
| 4ctj | SAM | Genome polyprotein | / | 0.659 | |
| 4rtm | SAM | DNA adenine methylase | 2.1.1.72 | 0.659 | |
| 5je2 | SAH | Methyl transferase | / | 0.659 | |
| 1g38 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.658 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.658 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.658 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.657 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.657 | |
| 1nw6 | SFG | Modification methylase RsrI | 2.1.1.72 | 0.656 | |
| 4k5r | FAD | Oxygenase | / | 0.656 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.655 | |
| 1pow | FAD | Pyruvate oxidase | 1.2.3.3 | 0.655 | |
| 1uay | ADN | Oxidoreductase | / | 0.655 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.655 | |
| 3alm | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.655 | |
| 3nt6 | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.655 | |
| 5il1 | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.655 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.655 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.654 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.654 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.654 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.654 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.654 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.654 | |
| 4ctk | SAM | Genome polyprotein | / | 0.654 | |
| 4tlx | FDA | KtzI | / | 0.654 | |
| 1nhp | FAD | NADH peroxidase | 1.11.1.1 | 0.653 | |
| 2px5 | SAH | Genome polyprotein | 2.7.7.48 | 0.653 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.653 | |
| 3lst | SAH | CalO1 | / | 0.653 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.653 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.653 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.653 | |
| 4qi4 | FAD | Cellobiose dehydrogenase | / | 0.653 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.653 | |
| 1npx | FAD | NADH peroxidase | 1.11.1.1 | 0.652 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.652 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.652 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.652 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.652 | |
| 4tm3 | FAD | KtzI | / | 0.652 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.652 | |
| 2cww | SAH | Uncharacterized protein | / | 0.651 | |
| 2npx | FAD | NADH peroxidase | 1.11.1.1 | 0.651 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.651 | |
| 3wv8 | ATP | Hmd co-occurring protein HcgE | / | 0.651 | |
| 4blw | SAH | Ribosomal RNA large subunit methyltransferase J | / | 0.651 | |
| 4gol | SA8 | DNA adenine methylase | 2.1.1.72 | 0.651 | |
| 4yv0 | S4M | Spermidine synthase, putative | / | 0.651 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.650 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.650 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.650 | |
| 2yr4 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.650 | |
| 3oz2 | FAD | Digeranylgeranylglycerophospholipid reductase | / | 0.650 | |
| 4tm1 | FDA | KtzI | / | 0.650 |