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 |
|---|---|---|---|
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 1.142 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.933 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.905 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.885 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.869 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.866 | |
| 3cbg | SAH | O-methyltransferase | / | 0.859 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.849 | |
| 3c3y | SAH | O-methyltransferase | / | 0.847 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.842 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.828 | |
| 3tos | SAH | CalS11 | / | 0.812 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.804 | |
| 3tr6 | SAH | O-methyltransferase | / | 0.791 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.790 | |
| 4gf5 | SAH | CalS11 | / | 0.789 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.780 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.763 | |
| 2plw | SAM | Ribosomal RNA methyltransferase, putative | / | 0.761 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.757 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.755 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.754 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.754 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.745 | |
| 3vyw | SAM | Uncharacterized protein | / | 0.745 | |
| 3lga | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.744 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.740 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.739 | |
| 5je2 | SAH | Methyl transferase | / | 0.739 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.734 | |
| 3hvk | 719 | Catechol O-methyltransferase | 2.1.1.6 | 0.734 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.732 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.731 | |
| 4blw | SAH | Ribosomal RNA large subunit methyltransferase J | / | 0.730 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.730 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.730 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.729 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.729 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.728 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.727 | |
| 1af7 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.724 | |
| 4blv | SAM | Ribosomal RNA large subunit methyltransferase J | / | 0.723 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.721 | |
| 5jdz | SAH | Methyl transferase | / | 0.721 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.720 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.720 | |
| 3axt | SAM | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.720 | |
| 3emd | SFG | Methyltransferase | / | 0.719 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.719 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.718 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.717 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.717 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.715 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.715 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.715 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.715 | |
| 3r6t | LU1 | Catechol O-methyltransferase | 2.1.1.6 | 0.714 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.713 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.713 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.713 | |
| 5je4 | SAH | Methyl transferase | / | 0.712 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.711 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.710 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.710 | |
| 4ctk | SAM | Genome polyprotein | / | 0.710 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.709 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.709 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.709 | |
| 5je3 | SAH | Methyl transferase | / | 0.709 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.706 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.706 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.706 | |
| 4n48 | SAM | Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 | 2.1.1.57 | 0.705 | |
| 3hvi | 619 | Catechol O-methyltransferase | 2.1.1.6 | 0.704 | |
| 1jr4 | CL4 | Catechol O-methyltransferase | 2.1.1.6 | 0.702 | |
| 2ji6 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.701 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.701 | |
| 3nwb | 659 | Catechol O-methyltransferase | 2.1.1.6 | 0.701 | |
| 2cww | SAH | Uncharacterized protein | / | 0.699 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.698 | |
| 3iv6 | SAM | Uncharacterized protein | / | 0.698 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.698 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.698 | |
| 5g3t | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.697 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.696 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.696 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.695 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.694 | |
| 2br5 | SAH | Cephalosporin hydroxylase CmcI | / | 0.694 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.694 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.694 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.693 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.692 | |
| 4j2w | FAD | Kynurenine 3-monooxygenase | / | 0.692 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.691 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.691 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.689 | |
| 3ka7 | FAD | Putative oxidoreductase | / | 0.689 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.688 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.688 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.687 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.687 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.687 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.687 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.686 | |
| 3a7d | FBN | Catechol O-methyltransferase | 2.1.1.6 | 0.686 | |
| 4j36 | FAD | Kynurenine 3-monooxygenase | / | 0.686 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.685 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.683 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.683 | |
| 3gyj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.683 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.683 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.683 | |
| 4ctj | SAM | Genome polyprotein | / | 0.682 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.681 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.679 | |
| 2xyr | SFG | Replicase polyprotein 1ab | 2.1.1 | 0.678 | |
| 3qft | NAP | NADPH--cytochrome P450 reductase | / | 0.678 | |
| 1khh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.677 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.677 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.677 | |
| 2px5 | SAH | Genome polyprotein | 2.7.7.48 | 0.677 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.674 | |
| 3s1s | SAH | Restriction endonuclease BpuSI | / | 0.674 | |
| 2ytz | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.673 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.673 | |
| 2bm9 | SAM | Cephalosporin hydroxylase CmcI | / | 0.672 | |
| 3lkz | SFG | Genome polyprotein | / | 0.672 | |
| 3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.672 | |
| 4poo | SAM | Putative RNA methylase | / | 0.672 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.671 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.670 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.670 | |
| 1p1b | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.668 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.668 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.668 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.668 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.668 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.668 | |
| 1e6e | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.667 | |
| 3nmu | SAM | Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase | / | 0.667 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.666 | |
| 5mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.666 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.665 | |
| 2hms | NAI | Ktr system potassium uptake protein A | / | 0.665 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.665 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.665 | |
| 3nwe | 662 | Catechol O-methyltransferase | 2.1.1.6 | 0.665 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.665 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.665 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.665 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.664 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.663 | |
| 1sus | SAH | Caffeoyl-CoA O-methyltransferase | 2.1.1.104 | 0.663 | |
| 3nw9 | 637 | Catechol O-methyltransferase | 2.1.1.6 | 0.663 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.663 | |
| 4uck | SAM | Large structural protein | / | 0.662 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.659 | |
| 3mj4 | FAD | UDP-galactopyranose mutase | / | 0.659 | |
| 2c4c | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.658 | |
| 2eq7 | NAD | Dihydrolipoyl dehydrogenase | / | 0.658 | |
| 4qi4 | FAD | Cellobiose dehydrogenase | / | 0.658 | |
| 4rto | SFG | DNA adenine methylase | 2.1.1.72 | 0.658 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.657 | |
| 3lby | SAH | Uncharacterized protein | / | 0.657 | |
| 4lv5 | ADP | Rhoptry protein 5B | / | 0.657 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.656 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.656 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.655 | |
| 3eva | SAH | Genome polyprotein | 2.1.1.56 | 0.655 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.655 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.654 | |
| 4eqw | FAD | Coenzyme A disulfide reductase | / | 0.654 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.653 | |
| 4guv | FAD | TetX family tetracycline inactivation enzyme | / | 0.653 | |
| 4k5r | FAD | Oxygenase | / | 0.653 | |
| 1k0l | FAD | p-hydroxybenzoate hydroxylase | / | 0.652 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.652 | |
| 3qgz | ADN | Histidine triad nucleotide-binding protein 1 | 3 | 0.652 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.652 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.652 | |
| 5jjs | SAH | Genome polyprotein | / | 0.652 | |
| 1hzz | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.651 | |
| 2pt6 | S4M | Spermidine synthase | / | 0.651 | |
| 2zzn | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.651 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.650 | |
| 4rtp | SAM | DNA adenine methylase | 2.1.1.72 | 0.650 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.650 |