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 |
|---|---|---|---|
| 1wwk | NAD | 307aa long hypothetical phosphoglycerate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1wwk | NAD | 307aa long hypothetical phosphoglycerate dehydrogenase | / | 1.000 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.572 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.536 | |
| 4ebf | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.527 | |
| 4xcv | NDP | Probable hydroxyacid dehydrogenase protein | / | 0.507 | |
| 2p9e | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.496 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.493 | |
| 4e5n | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.482 | |
| 4e5p | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.477 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.474 | |
| 3ijd | C2F | Methylenetetrahydrofolate reductase | / | 0.474 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.464 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 2p9g | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.461 | |
| 2pa3 | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.461 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.460 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 3zc3 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.460 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 4oag | ADP | Mitochondrial dynamics protein MID51 | / | 0.455 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.454 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.454 | |
| 5a3b | APR | SIR2 family protein | / | 0.453 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.451 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.450 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.450 | |
| 1yba | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.450 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.449 | |
| 3kb6 | NAD | D-lactate dehydrogenase | / | 0.449 | |
| 4e5k | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.449 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.449 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.448 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.447 | |
| 3baz | NAP | Hydroxyphenylpyruvate reductase | 1.1.1.237 | 0.447 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.446 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.446 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.446 | |
| 4nu6 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.446 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.445 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.445 | |
| 3mje | NDP | AmphB | / | 0.445 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.444 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.444 | |
| 3frq | ERY | Erythromycin resistance repressor protein | / | 0.444 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.443 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.443 | |
| 3uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.443 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.443 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.443 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.443 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.442 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.442 | |
| 3v2u | ATP | Protein GAL3 | / | 0.442 | |
| 4nxw | ADP | Mitochondrial dynamics protein MID51 | / | 0.442 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.441 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.441 | |
| 4nu5 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.441 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.441 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.440 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2h12 | CMX | Citrate synthase | / | 0.440 | |
| 2rkv | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.440 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.440 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.440 |