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 |
|---|---|---|---|
| 3dkv | AP5 | Adenylate kinase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3dkv | AP5 | Adenylate kinase | / | 1.000 | |
| 4qbi | AP5 | Adenylate kinase | / | 0.634 | |
| 2oo7 | AP5 | Adenylate kinase | / | 0.626 | |
| 3hpq | AP5 | Adenylate kinase | / | 0.624 | |
| 4qbh | AP5 | Adenylate kinase | / | 0.609 | |
| 2osb | AP5 | Adenylate kinase | / | 0.599 | |
| 4nu0 | AP5 | Adenylate kinase | / | 0.588 | |
| 4x8o | AP5 | Adenylate kinase | / | 0.586 | |
| 1p3j | AP5 | Adenylate kinase | / | 0.581 | |
| 1ank | ANP | Adenylate kinase | / | 0.579 | |
| 4jl6 | ADP | Adenylate kinase | / | 0.567 | |
| 1ake | AP5 | Adenylate kinase | / | 0.550 | |
| 4cf7 | ADP | Adenylate kinase | / | 0.549 | |
| 2eck | ADP | Adenylate kinase | / | 0.547 | |
| 2aky | AP5 | Adenylate kinase | / | 0.538 | |
| 4x8l | AP5 | Adenylate kinase | / | 0.534 | |
| 4jl5 | ADP | Adenylate kinase | / | 0.516 | |
| 2rgx | AP5 | Adenylate kinase | / | 0.507 | |
| 3tlx | ADP | Adenylate kinase 2 | / | 0.505 | |
| 2v3a | FAD | Rubredoxin-NAD(+) reductase | 1.18.1.1 | 0.480 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.477 | |
| 2zax | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.473 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.473 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.473 | |
| 2olr | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.469 | |
| 2bun | FAD | AppA protein | / | 0.467 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.466 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.465 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.462 | |
| 3vcy | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.462 | |
| 3cbs | R12 | Cellular retinoic acid-binding protein 2 | / | 0.461 | |
| 1p4a | PCP | Pur operon repressor | / | 0.460 | |
| 4ebf | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.460 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.460 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.460 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.459 | |
| 3swq | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.459 | |
| 2cbs | R13 | Cellular retinoic acid-binding protein 2 | / | 0.458 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.458 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.458 | |
| 2rl1 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.457 | |
| 2cdu | FAD | NADH oxidase | / | 0.456 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.456 | |
| 3ed1 | GA3 | Gibberellin receptor GID1 | / | 0.456 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.455 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.455 | |
| 1dbv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.454 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 2py7 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.453 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.453 | |
| 2bgl | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.452 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.452 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.452 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.452 | |
| 4die | C5P | Cytidylate kinase | / | 0.452 | |
| 4l9q | 9TP | Serum albumin | / | 0.452 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.451 | |
| 1j7k | ATP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.451 | |
| 1u8f | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.451 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.451 | |
| 4fhj | 0TZ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.450 | |
| 2j7p | GNP | Signal recognition particle protein | / | 0.450 | |
| 2j7p | GNP | Signal recognition particle receptor FtsY | / | 0.450 | |
| 2ooy | ATP | 5'-AMP-activated protein kinase subunit gamma | / | 0.450 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.449 | |
| 1vfr | FMN | Major NAD(P)H-flavin oxidoreductase | 1.6.99 | 0.449 | |
| 1pjk | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.448 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 4iwq | 1FV | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.448 | |
| 1cg6 | MTA | S-methyl-5'-thioadenosine phosphorylase | / | 0.447 | |
| 1kvu | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.447 | |
| 1xxj | UNC | Uricase | 1.7.3.3 | 0.447 | |
| 2ejz | SAH | Diphthine synthase | / | 0.447 | |
| 2yvw | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.447 | |
| 3r04 | UNQ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.447 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.447 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.447 | |
| 1zio | AP5 | Adenylate kinase | / | 0.446 | |
| 2i0a | MUI | Protease | / | 0.446 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.446 | |
| 3t3q | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.446 | |
| 4bdc | ODH | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.446 | |
| 1sxj | ADP | Replication factor C subunit 5 | / | 0.445 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.445 | |
| 3cgb | COA | Coenzyme A disulfide reductase | / | 0.445 | |
| 3mpt | 1GK | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 4okx | 198 | Androgen receptor | / | 0.445 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.445 | |
| 4x9m | FAD | Uncharacterized protein MG039 homolog | / | 0.445 | |
| 1fpq | SAM | Isoliquiritigenin 2'-O-methyltransferase | / | 0.444 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.444 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.444 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.444 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.444 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.443 | |
| 2acx | ANP | G protein-coupled receptor kinase 6 | 2.7.11.16 | 0.443 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.443 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.443 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 4dzz | ADP | Plasmid partitioning protein ParF | / | 0.443 | |
| 4h2n | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.443 | |
| 4kb8 | 1QO | Casein kinase I isoform delta | 2.7.11.1 | 0.443 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.442 | |
| 1sny | NAP | LD36273p | / | 0.442 | |
| 2e20 | B4P | Propionate kinase | / | 0.442 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.442 | |
| 4a6r | TA8 | Probable aminotransferase | / | 0.442 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.442 | |
| 5kgh | ACO | Predicted acetyltransferase | / | 0.442 | |
| 1g9c | BAB | Botulinum neurotoxin type B | 3.4.24.69 | 0.441 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.441 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.441 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 4eo3 | FMN | Bacterioferritin comigratory protein/NADH dehydrogenase | / | 0.441 | |
| 4fry | NAD | Putative signal-transduction protein with CBS domains | / | 0.441 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.441 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.441 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.440 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 1nvs | UCM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 1qrr | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.440 | |
| 2bxm | IMN | Serum albumin | / | 0.440 | |
| 2qbn | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.440 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.440 |