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 |
|---|---|---|---|
| 4lz8 | 1YX | Glutamate receptor 2 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4lz8 | 1YX | Glutamate receptor 2 | / | 1.000 | |
| 3rn8 | RN8 | Glutamate receptor 2 | / | 0.699 | |
| 3l9h | EMQ | Kinesin-like protein KIF11 | / | 0.493 | |
| 4blr | UTP | NTPase P4 | / | 0.481 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.473 | |
| 3vx4 | ATP | Putative ABC transporter, ATP-binding protein ComA | / | 0.468 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.467 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.467 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.465 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.464 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.463 | |
| 2f3e | AXQ | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.454 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.453 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.451 | |
| 5fl3 | ADP | Pili retraction protein PilT | / | 0.451 | |
| 4wbn | GTP | Tubulin alpha-1B chain | / | 0.450 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.449 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.449 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.449 | |
| 3pi5 | 3P5 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4brg | GNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.448 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.447 | |
| 3c21 | 2BA | DNA integrity scanning protein DisA | / | 0.447 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 1p3d | UMA | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.446 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.446 | |
| 4l4x | NDP | AmphI | / | 0.446 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.445 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.445 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.445 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.445 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.444 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.444 | |
| 4kb9 | G79 | Protease | / | 0.444 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.443 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3gu8 | 3GU | Death-associated protein kinase 1 | 2.7.11.1 | 0.443 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.443 | |
| 3vrb | FTN | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial | / | 0.443 | |
| 3vrb | FTN | Cytochrome b-large subunit | / | 0.443 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.443 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.442 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 2gr1 | FAD | Ferredoxin reductase | / | 0.441 | |
| 4ffb | GTP | Tubulin alpha-1 chain | / | 0.441 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.441 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.441 | |
| 4z26 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.441 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.440 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.440 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.440 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.440 |