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 |
|---|---|---|---|
| 4f6r | GDP | Tubulin beta chain |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4f6r | GDP | Tubulin beta chain | / | 1.000 | |
| 3zid | GDP | Tubulin-like protein CetZ | / | 0.588 | |
| 4b45 | GSP | Tubulin-like protein CetZ2 | / | 0.501 | |
| 5la6 | GDP | Tubulin beta-2B chain | / | 0.498 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.491 | |
| 2ex1 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.475 | |
| 3cb2 | GDP | Tubulin gamma-1 chain | / | 0.474 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.469 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.469 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.469 | |
| 2dgn | DOI | Adenylosuccinate synthetase isozyme 1 | / | 0.468 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.468 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.466 | |
| 4l4x | NDP | AmphI | / | 0.465 | |
| 4u3j | GTP | Tubulin beta chain | / | 0.465 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.464 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.463 | |
| 4a0r | DTB | Bifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial | 6.3.3.3 | 0.463 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.462 | |
| 1ra8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.461 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.461 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.460 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.460 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.460 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.459 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.458 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4fsl | 0VB | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.458 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.457 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.457 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.457 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.457 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.456 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.456 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.456 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.455 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.455 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.454 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.454 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.453 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.453 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.453 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.452 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.452 | |
| 2bto | GTP | Tubulin | / | 0.451 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.451 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.451 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.451 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.451 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.450 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.450 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.450 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.450 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.449 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.448 | |
| 1w4x | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.448 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.448 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.448 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.448 | |
| 5a3b | APR | SIR2 family protein | / | 0.448 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.447 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.447 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.447 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.447 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.446 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.446 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.446 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.445 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.445 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.445 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4u03 | GTP | Cyclic GMP-AMP synthase | / | 0.445 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.444 | |
| 2bfq | AR6 | [Protein ADP-ribosylglutamate] hydrolase AF_1521 | 3.2.2 | 0.444 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.444 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.444 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.444 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.444 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.444 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.444 | |
| 5jqg | GTP | Tubulin alpha-1B chain | / | 0.444 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.443 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.443 | |
| 3kmx | G00 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.443 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.443 | |
| 4dx7 | DM2 | Multidrug efflux pump subunit AcrB | / | 0.443 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.443 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.442 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 2gcq | DOI | Adenylosuccinate synthetase | / | 0.442 | |
| 3af3 | GCP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.442 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.442 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.442 | |
| 5ftf | ADP | TPR domain protein | / | 0.442 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.441 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.441 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.441 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.441 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.441 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.441 | |
| 2ilv | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.441 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.441 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.441 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.441 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.441 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.441 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.441 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.441 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.441 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.441 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.440 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.440 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.440 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.440 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.440 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.440 |