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 |
|---|---|---|---|
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 1.058 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 1.038 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.933 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.933 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.886 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.874 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.857 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.794 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.784 | |
| 3cbg | SAH | O-methyltransferase | / | 0.777 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.772 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.770 | |
| 3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.764 | |
| 3c3y | SAH | O-methyltransferase | / | 0.760 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.760 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.750 | |
| 4gf5 | SAH | CalS11 | / | 0.750 | |
| 3lga | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.745 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.745 | |
| 3tr6 | SAH | O-methyltransferase | / | 0.743 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.739 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.737 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.736 | |
| 3hvk | 719 | Catechol O-methyltransferase | 2.1.1.6 | 0.727 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.726 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.723 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.720 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.716 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.716 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.716 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.716 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.713 | |
| 1jr4 | CL4 | Catechol O-methyltransferase | 2.1.1.6 | 0.711 | |
| 3nwb | 659 | Catechol O-methyltransferase | 2.1.1.6 | 0.711 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.711 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.710 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.710 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.710 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.708 | |
| 3ea4 | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.708 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.708 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.707 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.706 | |
| 5d4u | SAM | Uncharacterized protein MJ0489 | / | 0.706 | |
| 2plw | SAM | Ribosomal RNA methyltransferase, putative | / | 0.705 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.705 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.705 | |
| 1khh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.704 | |
| 4blv | SAM | Ribosomal RNA large subunit methyltransferase J | / | 0.703 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.703 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.701 | |
| 4blw | SAH | Ribosomal RNA large subunit methyltransferase J | / | 0.701 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.700 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.699 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.699 | |
| 1y56 | FAD | 382aa long hypothetical sarcosine oxidase | / | 0.696 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.696 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.695 | |
| 1af7 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.694 | |
| 2cww | SAH | Uncharacterized protein | / | 0.694 | |
| 5je4 | SAH | Methyl transferase | / | 0.694 | |
| 3axt | SAM | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.693 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.693 | |
| 3vyw | SAM | Uncharacterized protein | / | 0.693 | |
| 4b69 | FAD | L-ornithine N(5)-monooxygenase | / | 0.693 | |
| 2ji6 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.692 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.692 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.692 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.691 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.691 | |
| 3a4t | SFG | tRNA (cytosine(48)-C(5))-methyltransferase | 2.1.1 | 0.690 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.690 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.690 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.689 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.687 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.687 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.687 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.687 | |
| 2xdo | FAD | TetX family tetracycline inactivation enzyme | / | 0.686 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.686 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.686 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.686 | |
| 4tm1 | FDA | KtzI | / | 0.686 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.686 | |
| 2yr4 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.685 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.685 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.682 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.681 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.681 | |
| 2c31 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.680 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.680 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.680 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.679 | |
| 2ytz | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.679 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.678 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.678 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.678 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.678 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.677 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.677 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.677 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.677 | |
| 1jkf | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.676 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.676 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.676 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.676 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.675 | |
| 1jki | NAI | Inositol-3-phosphate synthase | 5.5.1.4 | 0.675 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.674 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.674 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.674 | |
| 3nwe | 662 | Catechol O-methyltransferase | 2.1.1.6 | 0.673 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.673 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.672 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.672 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.672 | |
| 3p9u | FAD | TetX family tetracycline inactivation enzyme | / | 0.672 | |
| 3tos | SAH | CalS11 | / | 0.672 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.672 | |
| 4tm4 | FDA | KtzI | / | 0.672 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.672 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.670 | |
| 2ji7 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.670 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.670 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.669 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.669 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.668 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.668 | |
| 3emd | SFG | Methyltransferase | / | 0.668 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.668 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.667 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.667 | |
| 4guv | FAD | TetX family tetracycline inactivation enzyme | / | 0.667 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.667 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.667 | |
| 4g6h | NAI | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.666 | |
| 1ryi | FAD | Glycine oxidase | 1.4.3.19 | 0.665 | |
| 2cdu | ADP | NADH oxidase | / | 0.665 | |
| 2h39 | ADQ | ADP-glucose phosphorylase | / | 0.665 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.665 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.664 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.664 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.664 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.664 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.664 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.664 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.663 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.663 | |
| 3lov | FAD | Protoporphyrinogen oxidase | / | 0.663 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.662 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.662 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.662 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.661 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.660 | |
| 2x2r | X2O | Kinesin-like protein KIF11 | / | 0.660 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.660 | |
| 5d4v | SAH | Uncharacterized protein MJ0489 | / | 0.660 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.659 | |
| 2oy0 | SAH | Genome polyprotein | / | 0.658 | |
| 4dna | FAD | Probable glutathione reductase | / | 0.658 | |
| 5k7w | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.658 | |
| 1zq9 | SAM | Probable dimethyladenosine transferase | / | 0.657 | |
| 2br5 | SAH | Cephalosporin hydroxylase CmcI | / | 0.657 | |
| 2hms | NAI | Ktr system potassium uptake protein A | / | 0.657 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.657 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.657 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.656 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.656 | |
| 3s1s | SAH | Restriction endonuclease BpuSI | / | 0.656 | |
| 1k0l | FAD | p-hydroxybenzoate hydroxylase | / | 0.655 | |
| 1txz | APR | Probable ADP-ribose 1''-phosphate phosphatase YML087W | 3.1.3.84 | 0.655 | |
| 2zzn | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.654 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.654 | |
| 4hh4 | SAH | CcbJ | / | 0.654 | |
| 1ijh | FAD | Cholesterol oxidase | 1.1.3.6 | 0.653 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.653 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.653 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.653 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.653 | |
| 2g82 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.652 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.651 | |
| 4h0n | SAH | Dnmt2 | / | 0.651 | |
| 5jdz | SAH | Methyl transferase | / | 0.651 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.651 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.650 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.650 |