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 |
|---|---|---|---|
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.991 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.902 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.886 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.842 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.837 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.809 | |
| 3cbg | SAH | O-methyltransferase | / | 0.808 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.803 | |
| 3tr6 | SAH | O-methyltransferase | / | 0.775 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.762 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.757 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.756 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.755 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.749 | |
| 3hvk | 719 | Catechol O-methyltransferase | 2.1.1.6 | 0.741 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.736 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.733 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.731 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.730 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.728 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.727 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.726 | |
| 3c3y | SAH | O-methyltransferase | / | 0.725 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.724 | |
| 3nwb | 659 | Catechol O-methyltransferase | 2.1.1.6 | 0.724 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.724 | |
| 3lga | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.714 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.713 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.712 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.712 | |
| 5je2 | SAH | Methyl transferase | / | 0.712 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.710 | |
| 1jr4 | CL4 | Catechol O-methyltransferase | 2.1.1.6 | 0.708 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.708 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.706 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.705 | |
| 3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.705 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.705 | |
| 5g3t | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.705 | |
| 5jdz | SAH | Methyl transferase | / | 0.703 | |
| 2e1m | FAD | L-glutamate oxidase | / | 0.702 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.702 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.702 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.701 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.700 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.700 | |
| 1jnz | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.698 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.694 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.694 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.693 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.693 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.693 | |
| 4blw | SAH | Ribosomal RNA large subunit methyltransferase J | / | 0.693 | |
| 4e2x | SAH | Methyltransferase | / | 0.693 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.691 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.690 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.690 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.690 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.690 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.690 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.690 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.690 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.690 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.690 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.690 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.689 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.689 | |
| 4b69 | FAD | L-ornithine N(5)-monooxygenase | / | 0.689 | |
| 2fje | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.688 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.688 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.687 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.685 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.685 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.685 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.685 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.685 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.685 | |
| 3lkz | SFG | Genome polyprotein | / | 0.685 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.685 | |
| 3nn6 | FB0 | 6-hydroxy-L-nicotine oxidase | / | 0.685 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.684 | |
| 4u2l | SFD | Cholesterol oxidase | 1.1.3.6 | 0.684 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.684 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.683 | |
| 2ytz | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.682 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.682 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.680 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.680 | |
| 2plw | SAM | Ribosomal RNA methyltransferase, putative | / | 0.680 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.680 | |
| 3r6t | LU1 | Catechol O-methyltransferase | 2.1.1.6 | 0.680 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.680 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.678 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.678 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.678 | |
| 3vyw | SAM | Uncharacterized protein | / | 0.677 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.677 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.677 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.677 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.676 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.676 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.676 | |
| 4tm1 | FDA | KtzI | / | 0.676 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.676 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.675 | |
| 3oe4 | 610 | Catechol O-methyltransferase | 2.1.1.6 | 0.675 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.675 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.675 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.674 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.674 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.673 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.673 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.673 | |
| 3p9u | FAD | TetX family tetracycline inactivation enzyme | / | 0.673 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.673 | |
| 4ctj | SAM | Genome polyprotein | / | 0.673 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.672 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.672 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.672 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.672 | |
| 1ijh | FAD | Cholesterol oxidase | 1.1.3.6 | 0.671 | |
| 4tm4 | FDA | KtzI | / | 0.671 | |
| 4fx9 | FAD | Coenzyme A disulfide reductase | 1.8.1.14 | 0.670 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.669 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.669 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.669 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.669 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.669 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.668 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.668 | |
| 1reo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.667 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.667 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.667 | |
| 3k30 | ADP | Histamine dehydrogenase | / | 0.667 | |
| 4em4 | FAD | Coenzyme A disulfide reductase | / | 0.667 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.666 | |
| 1sus | SAH | Caffeoyl-CoA O-methyltransferase | 2.1.1.104 | 0.666 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.665 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.665 | |
| 4l7v | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.665 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.664 | |
| 3tos | SAH | CalS11 | / | 0.664 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.664 | |
| 3emd | SFG | Methyltransferase | / | 0.663 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.663 | |
| 1p1h | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.662 | |
| 3a7d | FBN | Catechol O-methyltransferase | 2.1.1.6 | 0.662 | |
| 3lov | FAD | Protoporphyrinogen oxidase | / | 0.662 | |
| 1tdk | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.661 | |
| 2jib | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.661 | |
| 2oy0 | SAH | Genome polyprotein | / | 0.661 | |
| 3wdm | ADN | 4-phosphopantoate--beta-alanine ligase | 6.3.2.36 | 0.661 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.661 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.660 | |
| 1zq9 | SAM | Probable dimethyladenosine transferase | / | 0.659 | |
| 2cww | SAH | Uncharacterized protein | / | 0.659 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.659 | |
| 3oe5 | 611 | Catechol O-methyltransferase | 2.1.1.6 | 0.659 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.658 | |
| 2cdu | ADP | NADH oxidase | / | 0.658 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.658 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.658 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.658 | |
| 4h0n | SAH | Dnmt2 | / | 0.658 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.657 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.657 | |
| 4aos | FAD | Steroid monooxygenase | / | 0.657 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.657 | |
| 5k7w | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.657 | |
| 1khh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.656 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.656 | |
| 2bm9 | SAM | Cephalosporin hydroxylase CmcI | / | 0.656 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.656 | |
| 4b65 | FAD | L-ornithine N(5)-monooxygenase | / | 0.655 | |
| 4mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.655 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.655 | |
| 1k0l | FAD | p-hydroxybenzoate hydroxylase | / | 0.654 | |
| 1nhr | FAD | NADH peroxidase | 1.11.1.1 | 0.654 | |
| 1pow | FAD | Pyruvate oxidase | 1.2.3.3 | 0.654 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.654 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.654 | |
| 4qi4 | FAD | Cellobiose dehydrogenase | / | 0.654 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.654 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.653 | |
| 3a4t | SFG | tRNA (cytosine(48)-C(5))-methyltransferase | 2.1.1 | 0.653 | |
| 4ctk | SAM | Genome polyprotein | / | 0.653 | |
| 4kvz | SAH | PtnL protein | / | 0.653 | |
| 1hzz | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.652 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.652 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.652 | |
| 3ozt | OZZ | Catechol O-methyltransferase | 2.1.1.6 | 0.652 | |
| 1gal | FAD | Glucose oxidase | 1.1.3.4 | 0.651 | |
| 1ty8 | ADP | Probable ADP-ribose 1''-phosphate phosphatase YML087W | 3.1.3.84 | 0.651 | |
| 3nwe | 662 | Catechol O-methyltransferase | 2.1.1.6 | 0.651 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.651 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.651 | |
| 1y56 | FAD | 382aa long hypothetical sarcosine oxidase | / | 0.650 | |
| 2g82 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.650 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.650 |