sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3m2r | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3m2r | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 1.000 | |
| 3m2r | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 1.000 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.836 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.836 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.779 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.779 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.643 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.630 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.611 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.611 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.487 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.482 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.463 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.463 | |
| 1h65 | GDP | Translocase of chloroplast 34 | 3.6.5 | 0.461 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.458 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.457 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.455 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.455 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.455 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.454 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.453 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.453 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.452 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.451 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.451 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.451 | |
| 3mje | NDP | AmphB | / | 0.450 | |
| 1kfb | IGP | Tryptophan synthase alpha chain | / | 0.449 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.448 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.447 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.447 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.447 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.447 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.447 | |
| 1omo | NAD | Alanine dehydrogenase | / | 0.445 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.445 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.445 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.444 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.444 | |
| 1dnp | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.443 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.443 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.443 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.442 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.442 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.442 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.442 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.442 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.441 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.441 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.440 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.440 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.440 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.440 |