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 |
|---|---|---|---|
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 1.058 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 1.038 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.917 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.902 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.885 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.858 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.842 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.804 | |
| 3cbg | SAH | O-methyltransferase | / | 0.793 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.792 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.788 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.773 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.764 | |
| 3lga | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.761 | |
| 3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.761 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.761 | |
| 3c3y | SAH | O-methyltransferase | / | 0.760 | |
| 3tr6 | SAH | O-methyltransferase | / | 0.755 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.753 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.748 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.736 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.732 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.730 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.728 | |
| 2cww | SAH | Uncharacterized protein | / | 0.727 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.726 | |
| 3hvk | 719 | Catechol O-methyltransferase | 2.1.1.6 | 0.726 | |
| 4gf5 | SAH | CalS11 | / | 0.721 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.720 | |
| 4blv | SAM | Ribosomal RNA large subunit methyltransferase J | / | 0.719 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.719 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.716 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.715 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.712 | |
| 1jr4 | CL4 | Catechol O-methyltransferase | 2.1.1.6 | 0.711 | |
| 5je4 | SAH | Methyl transferase | / | 0.711 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.710 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.710 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.710 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.710 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.709 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.709 | |
| 5je3 | SAH | Methyl transferase | / | 0.709 | |
| 3axt | SAM | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.708 | |
| 3ea4 | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.708 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.706 | |
| 2plw | SAM | Ribosomal RNA methyltransferase, putative | / | 0.705 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.705 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.703 | |
| 3e9y | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.702 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.702 | |
| 5jdz | SAH | Methyl transferase | / | 0.702 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.701 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.700 | |
| 1y56 | FAD | 382aa long hypothetical sarcosine oxidase | / | 0.699 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.699 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.699 | |
| 5g3t | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.699 | |
| 2ytz | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.697 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.696 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.695 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.694 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.693 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.693 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.693 | |
| 2ji6 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.692 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.692 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.691 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.691 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.691 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.691 | |
| 1jnz | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.690 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.690 | |
| 3nwb | 659 | Catechol O-methyltransferase | 2.1.1.6 | 0.690 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.690 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.689 | |
| 3vyw | SAM | Uncharacterized protein | / | 0.689 | |
| 3tos | SAH | CalS11 | / | 0.688 | |
| 5d4u | SAM | Uncharacterized protein MJ0489 | / | 0.688 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.687 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.687 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.687 | |
| 4tlx | FDA | KtzI | / | 0.687 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.687 | |
| 1khh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.686 | |
| 2xdo | FAD | TetX family tetracycline inactivation enzyme | / | 0.686 | |
| 2yr4 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.686 | |
| 4blw | SAH | Ribosomal RNA large subunit methyltransferase J | / | 0.686 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.686 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.686 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.686 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.685 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.685 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.684 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.684 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.684 | |
| 3emd | SFG | Methyltransferase | / | 0.683 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.683 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.682 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.682 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.682 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.682 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.682 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.681 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.680 | |
| 2np6 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.680 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.680 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.680 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.679 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.679 | |
| 2ji7 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.678 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.678 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.678 | |
| 1jkf | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.676 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.676 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.676 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.676 | |
| 1jki | NAI | Inositol-3-phosphate synthase | 5.5.1.4 | 0.675 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.675 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.675 | |
| 2x2r | X2O | Kinesin-like protein KIF11 | / | 0.675 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.674 | |
| 3a4t | SFG | tRNA (cytosine(48)-C(5))-methyltransferase | 2.1.1 | 0.674 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.674 | |
| 3nwe | 662 | Catechol O-methyltransferase | 2.1.1.6 | 0.673 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.673 | |
| 5k7w | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.673 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.672 | |
| 4kvz | SAH | PtnL protein | / | 0.672 | |
| 4tm4 | FDA | KtzI | / | 0.672 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.672 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.671 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.671 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.671 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.671 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.671 | |
| 4b69 | FAD | L-ornithine N(5)-monooxygenase | / | 0.670 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.670 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.668 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.668 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.668 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.667 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.667 | |
| 4g6h | NAI | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.666 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.665 | |
| 2cdu | ADP | NADH oxidase | / | 0.665 | |
| 2h39 | ADQ | ADP-glucose phosphorylase | / | 0.665 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.665 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.664 | |
| 2bm9 | SAM | Cephalosporin hydroxylase CmcI | / | 0.664 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.664 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.664 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.664 | |
| 3q9t | FAY | Uncharacterized protein | / | 0.664 | |
| 4guv | FAD | TetX family tetracycline inactivation enzyme | / | 0.664 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.663 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.663 | |
| 3lkz | SFG | Genome polyprotein | / | 0.663 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.663 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.662 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.662 | |
| 3cjq | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.662 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.662 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.661 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.661 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.660 | |
| 2fjb | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.659 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.659 | |
| 3rha | FDA | Putrescine oxidase | / | 0.659 | |
| 5je2 | SAH | Methyl transferase | / | 0.658 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.657 | |
| 2hms | NAI | Ktr system potassium uptake protein A | / | 0.657 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.657 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.657 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.657 | |
| 1zq9 | SAM | Probable dimethyladenosine transferase | / | 0.656 | |
| 3p9u | FAD | TetX family tetracycline inactivation enzyme | / | 0.656 | |
| 3s1s | SAH | Restriction endonuclease BpuSI | / | 0.656 | |
| 1k0l | FAD | p-hydroxybenzoate hydroxylase | / | 0.655 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.655 | |
| 4hh4 | SAH | CcbJ | / | 0.655 | |
| 3oe5 | 611 | Catechol O-methyltransferase | 2.1.1.6 | 0.654 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.654 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.653 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.653 | |
| 3swr | SFG | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.653 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.653 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.652 | |
| 2g82 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.652 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.652 | |
| 4dna | FAD | Probable glutathione reductase | / | 0.652 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.652 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.651 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.650 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.650 | |
| 4h0n | SAH | Dnmt2 | / | 0.650 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.650 |