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 |
|---|---|---|---|
| 5i39 | FAD | L-amino acid deaminase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 5i39 | FAD | L-amino acid deaminase | / | 1.000 | |
| 2qcu | FAD | Aerobic glycerol-3-phosphate dehydrogenase | 1.1.5.3 | 0.503 | |
| 3axb | FAD | Putative oxidoreductase | / | 0.498 | |
| 4bk3 | FAD | Probable salicylate monooxygenase | / | 0.482 | |
| 2c3c | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.479 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.476 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.475 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.471 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.471 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.469 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.468 | |
| 3tqc | ADP | Pantothenate kinase | / | 0.466 | |
| 1mo9 | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.465 | |
| 3nwz | COA | BH2602 protein | / | 0.465 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.464 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.463 | |
| 5cdt | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.459 | |
| 4gkv | NAD | Alcohol dehydrogenase, propanol-preferring | 1.1.1.1 | 0.458 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.457 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.457 | |
| 4ien | COA | Putative acyl-CoA hydrolase | / | 0.457 | |
| 1n06 | ADP | Riboflavin kinase | 2.7.1.26 | 0.456 | |
| 4l4x | NDP | AmphI | / | 0.456 | |
| 4ysh | FAD | Glycine oxidase | / | 0.456 | |
| 5kjc | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.456 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.454 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.454 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.454 | |
| 2bi8 | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.453 | |
| 3b20 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.453 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.453 | |
| 1tde | FAD | Thioredoxin reductase | 1.8.1.9 | 0.452 | |
| 5cds | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.452 | |
| 3w6u | NAP | 6-phosphogluconate dehydrogenase, NAD-binding protein | / | 0.451 | |
| 4bk2 | FAD | Probable salicylate monooxygenase | / | 0.451 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4nu5 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.451 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.450 | |
| 5j60 | FAD | Thioredoxin reductase | / | 0.450 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.449 | |
| 3rf7 | NAD | Iron-containing alcohol dehydrogenase | / | 0.449 | |
| 5kje | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.449 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.447 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.447 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.447 | |
| 1f0x | FAD | D-lactate dehydrogenase | 1.1.1.28 | 0.446 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.446 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.446 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.446 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.446 | |
| 4kcf | AKM | FAD-dependent oxidoreductase | / | 0.446 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.445 | |
| 4hai | I23 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.445 | |
| 4mo2 | FDA | UDP-galactopyranose mutase | / | 0.445 | |
| 5kj1 | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 3l8k | ADP | Dihydrolipoamide dehydrogenase (PdhD-3) | / | 0.444 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.444 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
| 5cdg | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.443 | |
| 2jdt | I5S | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 2tps | TPS | Thiamine-phosphate synthase | / | 0.443 | |
| 2v3a | FAD | Rubredoxin-NAD(+) reductase | 1.18.1.1 | 0.443 | |
| 3g7j | GTX | Glutathione transferase GST1-4 | / | 0.443 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.443 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.442 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.442 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.442 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.442 | |
| 4nfh | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 5fs7 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.442 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.441 | |
| 2bi7 | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.441 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.441 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.441 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.441 | |
| 2vce | U2F | UDP-glycosyltransferase 72B1 | / | 0.441 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.441 | |
| 4yjd | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.441 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.441 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1reo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.440 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.440 | |
| 2p2b | PRX | Acetyl-coenzyme A synthetase | / | 0.440 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.440 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.440 | |
| 4b2g | V1N | Uncharacterized protein | / | 0.440 | |
| 4kx6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.440 | |
| 4x9n | FAD | Uncharacterized protein MG039 homolog | / | 0.440 |