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 |
|---|---|---|---|
| 3rqh | B6P | ADP-dependent (S)-NAD(P)H-hydrate dehydratase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3rqh | B6P | ADP-dependent (S)-NAD(P)H-hydrate dehydratase | / | 1.000 | |
| 3rq6 | APR | ADP-dependent (S)-NAD(P)H-hydrate dehydratase | / | 0.642 | |
| 3rq8 | AP5 | ADP-dependent (S)-NAD(P)H-hydrate dehydratase | / | 0.571 | |
| 3rqq | BA3 | ADP-dependent (S)-NAD(P)H-hydrate dehydratase | / | 0.543 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.509 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.475 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.473 | |
| 5dp2 | NAP | CurF | / | 0.471 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.470 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.469 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.468 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.466 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.464 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.462 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.461 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.460 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.459 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.458 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.458 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.457 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.457 | |
| 4eki | 0QK | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.457 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.455 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.455 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.455 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.455 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.454 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.453 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.452 | |
| 2ejk | SAH | Diphthine synthase | / | 0.452 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.452 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.452 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.452 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.452 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.451 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.450 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.449 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.449 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.449 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.449 | |
| 3wag | TYD | Glycosyltransferase | / | 0.449 | |
| 4i02 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.449 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.448 | |
| 5ar4 | SB2 | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.448 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.447 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.447 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.447 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.447 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.446 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.446 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.445 | |
| 3uqd | ADP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.445 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.445 | |
| 1zdw | FLV | Prenyltransferase | / | 0.444 | |
| 2a7r | 5GP | GMP reductase 2 | / | 0.444 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.444 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.444 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.443 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.443 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.443 | |
| 2nni | MTK | Cytochrome P450 2C8 | / | 0.443 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.443 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.443 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.443 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.443 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.443 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.442 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.442 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.442 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.442 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.442 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.442 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.442 | |
| 4g9k | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.442 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.441 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.441 | |
| 2ejz | SAH | Diphthine synthase | / | 0.441 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.441 | |
| 3ump | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.441 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.441 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.440 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.440 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.440 | |
| 2zaw | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 0.440 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.440 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.440 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4c72 | TLG | 3-oxoacyl-ACP synthase | / | 0.440 | |
| 4f32 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | / | 0.440 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.440 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.440 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 |