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 |
|---|---|---|---|
| 1p84 | UQ6 | Cytochrome b |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1p84 | UQ6 | Cytochrome b | / | 1.000 | |
| 2ibz | UQ6 | Cytochrome b | / | 0.644 | |
| 1ezv | UQ6 | Cytochrome b | / | 0.634 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.485 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.483 | |
| 3uku | C69 | Actin-related protein 3 | / | 0.477 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.475 | |
| 2trt | TAC | Tetracycline repressor protein class D | / | 0.473 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.471 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.470 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.470 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.470 | |
| 2xpv | MIY | Tetracycline repressor protein class D | / | 0.470 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.470 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.468 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.468 | |
| 2gby | BRN | HTH-type transcriptional regulator QacR | / | 0.467 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.467 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.467 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 3hx4 | ANP | Calmodulin-domain protein kinase 1 | / | 0.465 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.465 | |
| 4rrr | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.465 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.465 | |
| 5fkm | TDC | Tetracycline repressor protein class D | / | 0.465 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.464 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.464 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.463 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.463 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.463 | |
| 1uyu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.462 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 3hek | BD0 | Heat shock protein HSP 90-alpha | / | 0.462 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.461 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.461 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.461 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.461 | |
| 4g9k | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.461 | |
| 4kz0 | 1UJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.461 | |
| 4d7m | TDC | Tetracycline repressor protein class D | / | 0.460 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.460 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.460 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.459 | |
| 3lm9 | ADP | Putative fructokinase | 2.7.1.4 | 0.459 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.459 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.459 | |
| 4c3f | 7KW | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.459 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 2cgp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.458 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.458 | |
| 4k33 | ACP | Fibroblast growth factor receptor 3 | 2.7.10.1 | 0.458 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.457 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.457 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.457 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.457 | |
| 2y3s | TIR | TamL | / | 0.457 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.457 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.457 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.457 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.456 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.456 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.456 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.456 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.455 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.455 | |
| 3oqu | A8S | Abscisic acid receptor PYL9 | / | 0.455 | |
| 4jhz | 1KV | Beta-glucuronidase | 3.2.1.31 | 0.455 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.455 | |
| 1gae | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.454 | |
| 1yrd | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.454 | |
| 3dey | DHT | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.454 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3klm | DHT | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.454 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.454 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.454 | |
| 4i0b | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.454 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 3q3c | NAD | NAD-dependent L-serine dehydrogenase | / | 0.453 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.453 | |
| 4gk2 | L66 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.453 | |
| 1w0k | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.452 | |
| 1w0k | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.452 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.452 | |
| 2jbs | FMN | p-hydroxyphenylacetate 3-hydroxylase, oxygenase component | / | 0.452 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.452 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.452 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 4iq7 | 1G9 | Mycocyclosin synthase | 1.14.21.9 | 0.452 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.451 | |
| 1omo | NAD | Alanine dehydrogenase | / | 0.451 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.451 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.451 | |
| 3r04 | UNQ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.451 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 4ng4 | ADP | Phosphoglycerate kinase | / | 0.451 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1feb | FAD | Trypanothione reductase | 1.8.1.12 | 0.450 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.450 | |
| 3wrl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.450 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.449 | |
| 1dss | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.449 | |
| 1hdg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.449 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.449 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 4abz | T1C | Tetracycline repressor protein class D | / | 0.449 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.449 | |
| 4f9m | FCM | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.449 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1fea | FAD | Trypanothione reductase | 1.8.1.12 | 0.448 | |
| 1nvq | UCN | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.448 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.448 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.448 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.447 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 2jk6 | FAD | Trypanothione reductase | / | 0.447 | |
| 2x6o | 2TC | Tetracycline repressor protein class D | / | 0.447 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.447 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.447 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.447 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.447 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.447 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.447 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.447 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.446 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.446 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.446 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.446 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.446 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.446 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.446 | |
| 4xj4 | 3AT | Cyclic GMP-AMP synthase | / | 0.446 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.445 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.445 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.445 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.445 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.445 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3qw2 | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.445 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.445 | |
| 4g3p | UD1 | Bifunctional protein GlmU | / | 0.445 | |
| 1bgq | RDC | ATP-dependent molecular chaperone HSP82 | / | 0.444 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.444 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.444 | |
| 1fdo | MGD | Formate dehydrogenase H | 1.1.99.33 | 0.444 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.444 | |
| 1hdr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.444 | |
| 1mc1 | PCX | Carboxyethyl-arginine beta-lactam-synthase | 6.3.3.4 | 0.444 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 3kjm | 245 | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.444 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.444 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.444 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.444 | |
| 4kip | 1R9 | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 5fkl | TDC | Tetracycline repressor protein class D | / | 0.444 | |
| 5itz | GTP | Tubulin alpha-1B chain | / | 0.444 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.443 | |
| 1iy8 | NAD | Levodione reductase | / | 0.443 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.443 | |
| 2v5a | LZL | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 2x7j | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.443 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.443 | |
| 3id8 | MRK | Glucokinase | 2.7.1.2 | 0.443 | |
| 3nyr | MLC | Putative fatty acid synthase | / | 0.443 | |
| 3p0h | FSE | Putative tyrosyl-tRNA synthetase | / | 0.443 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.443 | |
| 4ge9 | 0L0 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.443 | |
| 4ihl | 1F5 | 14-3-3 protein zeta/delta | / | 0.443 | |
| 1ra3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 2gcq | DOI | Adenylosuccinate synthetase | / | 0.442 | |
| 2h94 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.442 | |
| 2uuv | FAD | Alkyldihydroxyacetonephosphate synthase | 2.5.1.26 | 0.442 | |
| 2xab | VHD | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.442 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.442 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3wrh | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.442 | |
| 4oae | CLM | Uncharacterized protein | / | 0.442 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.441 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.441 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 3gxo | MQA | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.441 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.441 | |
| 4aux | XTC | Tetracycline repressor protein class D | / | 0.441 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.441 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.441 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.441 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.441 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.441 | |
| 4xgx | ADP | FAD:protein FMN transferase | / | 0.441 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.440 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2vkv | TDC | Tetracycline repressor protein class D | / | 0.440 | |
| 2vr1 | ATF | Biotin carboxylase | 6.3.4.14 | 0.440 | |
| 2vzz | SCA | Putative succinyl-CoA transferase Rv0802c | 2.8.3 | 0.440 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.440 | |
| 4i02 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.440 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.440 | |
| 4qq3 | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.440 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.440 |