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 |
|---|---|---|---|
| 3b2s | B2S | Trichothecene 3-O-acetyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3b2s | B2S | Trichothecene 3-O-acetyltransferase | / | 1.000 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.502 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.500 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.495 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.489 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.485 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.476 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.475 | |
| 3gvi | ADP | Malate dehydrogenase | / | 0.474 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.472 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.472 | |
| 2nni | MTK | Cytochrome P450 2C8 | / | 0.471 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.469 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.469 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.468 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.467 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.466 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.466 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.466 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.465 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.463 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.463 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.463 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 1k6v | XN2 | Gag-Pol polyprotein | 3.4.23.16 | 0.462 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.462 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.462 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.461 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.461 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 4fhf | 0TT | Spore photoproduct lyase | / | 0.460 | |
| 1gpd | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.459 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.458 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.458 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.458 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.457 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.457 | |
| 2gmv | PEP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.457 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.457 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.457 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.457 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.456 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.456 | |
| 3gob | HXX | DdmC | / | 0.456 | |
| 4ynt | FDA | Glucose oxidase, putative | / | 0.456 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1yrd | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.455 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.455 | |
| 2qbn | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.455 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.455 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.455 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.455 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.455 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.454 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.454 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.454 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.453 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.453 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.453 | |
| 4l4x | NDP | AmphI | / | 0.453 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.452 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.452 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3e8x | NAP | BH1520 protein | / | 0.452 | |
| 4g3r | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.452 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.452 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.452 | |
| 2ehu | NAD | 1-pyrroline-5-carboxylate dehydrogenase | / | 0.451 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.451 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.450 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.450 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.450 | |
| 4bmo | FMN | Protein NrdI | / | 0.450 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.449 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.449 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.449 | |
| 4l8u | 9AZ | Serum albumin | / | 0.449 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.449 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.449 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.448 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.448 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.448 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.448 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.448 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.448 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.448 | |
| 1guy | NAD | Malate dehydrogenase | / | 0.447 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.447 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4jhz | 1KV | Beta-glucuronidase | 3.2.1.31 | 0.447 | |
| 4xgi | NAD | Glutamate dehydrogenase | / | 0.447 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.446 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1wp4 | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.446 | |
| 2hy8 | 1ST | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.446 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.446 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.446 | |
| 3t2v | KKJ | Peptidoglycan recognition protein 1 | / | 0.446 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.445 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.445 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.445 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.445 | |
| 1a27 | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.444 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.444 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.444 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.443 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.443 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.443 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.443 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.443 | |
| 3wrh | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.443 | |
| 4f9f | GDP | Putative glycosyltransferase | / | 0.443 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.442 | |
| 2eud | GCQ | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.442 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3h3f | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.442 | |
| 3ntd | COA | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.442 | |
| 3opd | HIE | Heat shock protein 83 | / | 0.442 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.442 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.442 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.442 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.441 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.441 | |
| 2cgp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.441 | |
| 2ejz | SAH | Diphthine synthase | / | 0.441 | |
| 2j09 | FMN | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.441 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.441 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.441 | |
| 2y4g | TIR | TamL | / | 0.441 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.441 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.441 | |
| 5dhh | DGW | Nociceptin receptor | / | 0.441 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.440 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.440 | |
| 1z1f | STL | Resveratrol synthase | / | 0.440 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.440 | |
| 2gna | GDU | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.440 | |
| 2vwh | NAP | Glucose 1-dehydrogenase | / | 0.440 | |
| 2xvq | 9DS | Serum albumin | / | 0.440 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.440 | |
| 3ras | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.440 | |
| 3w8w | FAD | Putative FAD-dependent oxygenase EncM | / | 0.440 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.440 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.440 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.440 | |
| 4u7w | NDP | MxaA | / | 0.440 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.440 |