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 |
|---|---|---|---|
| 2p8u | COA | Hydroxymethylglutaryl-CoA synthase, cytoplasmic | 2.3.3.10 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2p8u | COA | Hydroxymethylglutaryl-CoA synthase, cytoplasmic | 2.3.3.10 | 1.000 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.565 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.555 | |
| 2wya | HMG | Hydroxymethylglutaryl-CoA synthase, mitochondrial | 2.3.3.10 | 0.554 | |
| 5hwp | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.517 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.515 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.514 | |
| 1ysl | COA | Hydroxymethylglutaryl-CoA synthase | 2.3.3.10 | 0.486 | |
| 4l4x | NDP | AmphI | / | 0.484 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.482 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.470 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.468 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.467 | |
| 1rek | B8L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.465 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.464 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.463 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.462 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.461 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.461 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.460 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.460 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.458 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.458 | |
| 1ppj | ANY | Cytochrome b | / | 0.457 | |
| 2fa3 | ACO | Hydroxymethylglutaryl-CoA synthase | / | 0.457 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.456 | |
| 2ath | 3EA | Peroxisome proliferator-activated receptor gamma | / | 0.456 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.456 | |
| 3eks | CY9 | Actin-5C | / | 0.456 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.454 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.454 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.454 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.454 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.453 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.453 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.452 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.452 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.451 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.451 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.451 | |
| 2cgw | 3C3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.450 | |
| 3ful | 52D | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.450 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.450 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.450 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.449 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.449 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.448 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.447 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.447 | |
| 3eku | CY9 | Actin-5C | / | 0.447 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.447 | |
| 2e8r | SAH | Diphthine synthase | / | 0.446 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.446 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 2ejz | SAH | Diphthine synthase | / | 0.445 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.445 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.445 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.444 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.444 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.444 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.444 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.444 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.443 | |
| 1osv | CHC | Bile acid receptor | / | 0.443 | |
| 2hej | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.443 | |
| 3bbr | BHY | Glutamate receptor 2 | / | 0.443 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.443 | |
| 3fun | 798 | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.443 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.443 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2e7r | SAH | Diphthine synthase | / | 0.442 | |
| 2ehl | SAH | Diphthine synthase | / | 0.442 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.442 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.442 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.442 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.442 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.442 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.442 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.442 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.442 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.442 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.442 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 2e4n | SAH | Diphthine synthase | / | 0.441 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.441 | |
| 3skg | PB8 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.441 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.441 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.441 | |
| 4pmj | NAP | Putative oxidoreductase | / | 0.441 | |
| 1daa | PLP | D-alanine aminotransferase | 2.6.1.21 | 0.440 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.440 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.440 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.440 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.440 | |
| 2p20 | PRX | Acetyl-coenzyme A synthetase | / | 0.440 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.440 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.440 | |
| 2yph | QQY | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.440 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.440 | |
| 3toh | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 4a31 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4qxr | 1YE | Stimulator of interferon genes protein | / | 0.440 |