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 Sites are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 1.000 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 1.000 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.859 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.732 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.685 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.685 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.650 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.650 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.508 | |
| 3m2r | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.503 | |
| 3m2r | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.503 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.482 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.475 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.475 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.472 | |
| 3own | 3OX | Renin | 3.4.23.15 | 0.471 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.471 | |
| 4yp6 | NAP | Nicotinamide-nucleotide adenylyltransferase | 2.7.7.1 | 0.470 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.469 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.469 | |
| 3u9e | COA | Lmo1369 protein | / | 0.468 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.467 | |
| 3muo | ZPR | Prolyl endopeptidase | / | 0.466 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.465 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.465 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.465 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.465 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.462 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.462 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.460 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.458 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.456 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.456 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.455 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.455 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.455 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.454 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.453 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.453 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.453 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.452 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.452 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.451 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.450 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.450 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.449 | |
| 5bur | ATP | 2-succinylbenzoate--CoA ligase | / | 0.449 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.448 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.448 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.448 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.447 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.447 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.447 | |
| 2r59 | PH0 | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.447 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.446 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.446 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.445 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.445 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.445 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.445 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.444 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.444 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.443 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.443 | |
| 2ilv | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.443 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.443 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.443 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.443 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.442 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.442 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.442 | |
| 3a3g | DLZ | Lumazine protein | / | 0.442 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.442 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.442 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.442 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1obb | NAD | Alpha-glucosidase | 3.2.1.20 | 0.441 | |
| 1ooq | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.441 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.441 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.441 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.441 | |
| 2xfs | J01 | Uncharacterized protein | / | 0.440 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.440 | |
| 3s8p | SAM | Histone-lysine N-methyltransferase KMT5B | 2.1.1.43 | 0.440 |