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 |
|---|---|---|---|
| 4j5r | A1R | O-acetyl-ADP-ribose deacetylase 1 | 3.5.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4j5r | A1R | O-acetyl-ADP-ribose deacetylase 1 | 3.5.1 | 1.000 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.486 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.482 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.479 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.478 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.476 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.475 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.473 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.470 | |
| 4dxh | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.470 | |
| 4xd2 | NAI | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.469 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.468 | |
| 3fcj | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.468 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.468 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.466 | |
| 5cdt | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.464 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.462 | |
| 4zla | BES | Cytosol aminopeptidase | 3.4.11.1 | 0.461 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.460 | |
| 5dp2 | NAP | CurF | / | 0.460 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.459 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.459 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.459 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.459 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.458 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.458 | |
| 4uir | FAD | Oleate hydratase | 4.2.1.53 | 0.457 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.456 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.456 | |
| 5cdg | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.456 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.455 | |
| 5kjf | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.455 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.454 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.454 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.454 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.454 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.453 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.452 | |
| 2ge3 | ACO | Probable acetyltransferase | / | 0.452 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.452 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.452 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.452 | |
| 5kcz | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.452 | |
| 2fzm | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.451 | |
| 2hej | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.451 | |
| 1e3l | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.450 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.450 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.450 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.450 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.450 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.449 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.449 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.449 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.449 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.449 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.448 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.448 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.448 | |
| 2h2a | DND | Probable nicotinate-nucleotide adenylyltransferase | / | 0.448 | |
| 3ll9 | ADP | Isopentenyl phosphate kinase | / | 0.448 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.447 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3r96 | ACO | MccE protein | / | 0.447 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.447 | |
| 5kj6 | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.447 | |
| 1p0f | NAP | NADP-dependent alcohol dehydrogenase | 1.1.1.2 | 0.446 | |
| 3e8n | VRA | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.446 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.446 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.446 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4dpl | NAP | Malonyl-CoA reductase | 1.2.1.75 | 0.446 | |
| 4kuh | CAA | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.446 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.446 | |
| 1adc | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.445 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.445 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.445 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.445 | |
| 4dwv | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.445 | |
| 4nfs | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 1f0x | FAD | D-lactate dehydrogenase | 1.1.1.28 | 0.444 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.444 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.444 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.444 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 4kx6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.444 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.444 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.443 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.443 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.443 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3ixk | 929 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.443 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.443 | |
| 4f9f | GDP | Putative glycosyltransferase | / | 0.443 | |
| 1cbq | RE9 | Cellular retinoic acid-binding protein 2 | / | 0.442 | |
| 2qfx | NDP | Isocitrate dehydrogenase [NADP], mitochondrial | 1.1.1.42 | 0.442 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.442 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.442 | |
| 3kgc | LY7 | Glutamate receptor 2 | / | 0.442 | |
| 3ms4 | 21N | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.442 | |
| 3suf | SUE | Polyprotein | / | 0.442 | |
| 3two | NDP | Mannitol dehydrogenase | / | 0.442 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.442 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.442 | |
| 1dap | NDP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.441 | |
| 1kf6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.441 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.441 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 2c0c | NAP | Prostaglandin reductase 3 | 1 | 0.441 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.441 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.441 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3mx5 | UTP | Nucleoprotein | / | 0.441 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.441 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 1llu | NAD | Alcohol dehydrogenase | / | 0.440 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.440 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.440 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.440 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.440 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.440 | |
| 4wso | NAD | Probable nicotinate-nucleotide adenylyltransferase | / | 0.440 |