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 |
|---|---|---|---|
| 4j5r | A1R | O-acetyl-ADP-ribose deacetylase 1 | 3.5.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4j5r | A1R | O-acetyl-ADP-ribose deacetylase 1 | 3.5.1 | 1.000 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.478 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.472 | |
| 4dxh | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.470 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.465 | |
| 2dgn | DOI | Adenylosuccinate synthetase isozyme 1 | / | 0.465 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.464 | |
| 4l4x | NDP | AmphI | / | 0.464 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.463 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.462 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.461 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.460 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.456 | |
| 2i7n | ACO | Pantothenate kinase 1 | 2.7.1.33 | 0.456 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.456 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.455 | |
| 2ge3 | ACO | Probable acetyltransferase | / | 0.454 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.454 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.453 | |
| 4uir | FAD | Oleate hydratase | 4.2.1.53 | 0.453 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.452 | |
| 3dl0 | AP5 | Adenylate kinase | / | 0.452 | |
| 5dp2 | NAP | CurF | / | 0.452 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.451 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.451 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.451 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.451 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.451 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.449 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.449 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.449 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 5kcz | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.449 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.448 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.448 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.447 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 5e5h | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.447 | |
| 1iy8 | NAD | Levodione reductase | / | 0.446 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.446 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.446 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.446 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.446 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.446 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.446 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.445 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.445 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.445 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.445 | |
| 5kjf | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.444 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.444 | |
| 2rgo | FAD | Alpha-Glycerophosphate Oxidase | / | 0.444 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.444 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.444 | |
| 2h2a | DND | Probable nicotinate-nucleotide adenylyltransferase | / | 0.443 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.443 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.443 | |
| 1cbq | RE9 | Cellular retinoic acid-binding protein 2 | / | 0.442 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.442 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.442 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.442 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.442 | |
| 2fzm | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.441 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.441 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.441 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.441 | |
| 1lol | XMP | Orotidine 5'-phosphate decarboxylase | 4.1.1.23 | 0.440 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.440 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.440 | |
| 3ixk | 929 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4dpl | NAP | Malonyl-CoA reductase | 1.2.1.75 | 0.440 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.440 | |
| 4nfs | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 | |
| 4qxq | 1YE | Stimulator of interferon genes protein | / | 0.440 | |
| 5kj6 | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 |