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 |
|---|---|---|---|
| 1f0y | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1f0y | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 1.000 | |
| 1il0 | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.622 | |
| 1m76 | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.600 | |
| 1m75 | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.598 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.528 | |
| 1hku | NAD | C-terminal-binding protein 1 | 1.1.1 | 0.527 | |
| 2hu2 | NAD | C-terminal binding protein 1 | / | 0.504 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.479 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.475 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.474 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.474 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.473 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.471 | |
| 2xb5 | I7T | Tetracycline repressor protein class D | / | 0.467 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.466 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.465 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.465 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.465 | |
| 3lqs | PSZ | D-alanine aminotransferase | 2.6.1.21 | 0.462 | |
| 4b0q | GMF | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.462 | |
| 1i6k | TYM | Tryptophan--tRNA ligase | 6.1.1.2 | 0.461 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.461 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.461 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.461 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1xnj | ADP | Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 | 2.7.1.25 | 0.460 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.460 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.460 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.459 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.459 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.459 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 1kvu | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.458 | |
| 3w2e | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.458 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.457 | |
| 4dx7 | DM2 | Multidrug efflux pump subunit AcrB | / | 0.457 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.457 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.456 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.456 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.456 | |
| 1k7l | 544 | Peroxisome proliferator-activated receptor alpha | / | 0.455 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.455 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.455 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.454 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1ra8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.454 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.454 | |
| 2p9g | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.454 | |
| 2xpv | MIY | Tetracycline repressor protein class D | / | 0.454 | |
| 3w8q | AGS | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.454 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.454 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.453 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.453 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.453 | |
| 3r83 | Z14 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.453 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.453 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.453 | |
| 4wji | NAP | Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase | / | 0.453 | |
| 5eso | ISC | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.453 | |
| 1c9k | 5GP | Bifunctional adenosylcobalamin biosynthesis protein CobU | / | 0.452 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.452 | |
| 2xrl | DXT | Tetracycline repressor protein class D | / | 0.452 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.452 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.452 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.452 | |
| 5fko | TDC | Tetracycline repressor protein class D | / | 0.452 | |
| 2i7p | ACO | Pantothenate kinase 3 | 2.7.1.33 | 0.451 | |
| 4l4x | NDP | AmphI | / | 0.451 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.450 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.450 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.450 | |
| 4y35 | F90 | Endothiapepsin | 3.4.23.22 | 0.450 | |
| 1kqn | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.449 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.449 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.449 | |
| 3k6l | 2BB | Peptide deformylase | 3.5.1.88 | 0.449 | |
| 3s87 | ADP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.449 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.448 | |
| 2tct | CTC | Tetracycline repressor protein class D | / | 0.448 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.448 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.448 | |
| 4ew3 | DXZ | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.448 | |
| 4lz8 | 1YX | Glutamate receptor 2 | / | 0.448 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.448 | |
| 4qbg | AP5 | Adenylate kinase | / | 0.448 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.447 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.447 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.447 | |
| 3a3g | DLZ | Lumazine protein | / | 0.447 | |
| 3gvi | ADP | Malate dehydrogenase | / | 0.447 | |
| 3p0h | FSE | Putative tyrosyl-tRNA synthetase | / | 0.447 | |
| 4abz | T1C | Tetracycline repressor protein class D | / | 0.447 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.447 | |
| 4yj2 | GTP | Tubulin alpha-1B chain | / | 0.447 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 2b53 | D23 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.446 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.446 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.446 | |
| 4gfv | PRO_GLU_LEU_THR_PTR | Tyrosine-protein phosphatase non-receptor type 18 | 3.1.3.48 | 0.446 | |
| 1dyh | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.445 | |
| 1h65 | GDP | Translocase of chloroplast 34 | 3.6.5 | 0.445 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.445 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.445 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.445 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.445 | |
| 3zly | YSO | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.445 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.445 | |
| 1ylu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.444 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.444 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.444 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.444 | |
| 3toz | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.444 | |
| 4eo3 | FMN | Bacterioferritin comigratory protein/NADH dehydrogenase | / | 0.444 | |
| 4kug | NAD | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.444 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.444 | |
| 1daa | PLP | D-alanine aminotransferase | 2.6.1.21 | 0.443 | |
| 2npx | FAD | NADH peroxidase | 1.11.1.1 | 0.443 | |
| 2xf3 | J01 | Uncharacterized protein | / | 0.443 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.443 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.443 | |
| 3ieu | GDP | GTPase Era | / | 0.443 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.443 | |
| 4fg8 | ATP | Calcium/calmodulin-dependent protein kinase type 1 | 2.7.11.17 | 0.443 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.443 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.443 | |
| 5fwn | NAP | Putative dehydrogenase | / | 0.443 | |
| 2ejz | SAH | Diphthine synthase | / | 0.442 | |
| 2fre | FMN | NAD(P)H-flavin oxidoreductase | / | 0.442 | |
| 2gmj | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.442 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.442 | |
| 2v3a | FAD | Rubredoxin-NAD(+) reductase | 1.18.1.1 | 0.442 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.442 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4fri | DWA | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4nvk | 2NY | Peroxidase | / | 0.442 | |
| 4xgx | ADP | FAD:protein FMN transferase | / | 0.442 | |
| 5fkl | TDC | Tetracycline repressor protein class D | / | 0.442 | |
| 1foa | UD1 | Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase | 2.4.1.101 | 0.441 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1kvk | ATP | Mevalonate kinase | 2.7.1.36 | 0.441 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.441 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.441 | |
| 1pvg | ANP | DNA topoisomerase 2 | 5.99.1.3 | 0.441 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.441 | |
| 2nua | COA | Succinate--CoA ligase [ADP-forming] subunit alpha | 6.2.1.5 | 0.441 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.441 | |
| 2o7o | DXT | Tetracycline repressor protein class D | / | 0.441 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.441 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.441 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1i24 | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.440 | |
| 1icu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.440 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2eud | GCQ | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.440 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.440 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.440 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.440 | |
| 2zvc | SAH | Precorrin-3 C17-methyltransferase | / | 0.440 | |
| 3a6r | FMN | FMN-binding protein | / | 0.440 | |
| 3d2m | COA | Amino-acid acetyltransferase | / | 0.440 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.440 | |
| 4gcm | NAP | Thioredoxin reductase | 1.8.1.9 | 0.440 | |
| 4lj6 | ACP | Chaperone protein ClpB | / | 0.440 | |
| 4lol | 1YE | Stimulator of interferon genes protein | / | 0.440 | |
| 4m2b | UPG | UDP-glucose pyrophosphorylase | / | 0.440 |