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 |
|---|---|---|---|
| 2ahv | COA | Acetate CoA-transferase YdiF | 2.8.3.8 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2ahv | COA | Acetate CoA-transferase YdiF | 2.8.3.8 | 1.000 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.478 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.469 | |
| 4eut | BX7 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.468 | |
| 3nww | 3NW | Mitogen-activated protein kinase 14 | / | 0.465 | |
| 4g2f | C07 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.465 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.463 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.462 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.461 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.461 | |
| 4jb1 | FAD | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.461 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.459 | |
| 3hll | I45 | Mitogen-activated protein kinase 14 | / | 0.459 | |
| 5eyp | LOC | Tubulin beta chain | / | 0.457 | |
| 2r7b | 253 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.456 | |
| 2v00 | V15 | Endothiapepsin | 3.4.23.22 | 0.456 | |
| 3a0t | ADP | Sensor histidine kinase | / | 0.456 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.456 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.456 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.456 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.456 | |
| 4aa4 | QC0 | Mitogen-activated protein kinase 14 | / | 0.454 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.453 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.453 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.453 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.453 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.452 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.452 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.452 | |
| 3u9e | COA | Lmo1369 protein | / | 0.452 | |
| 4yek | THM | Thymidine phosphorylase | / | 0.452 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.451 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.450 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.450 | |
| 1uu9 | BI3 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.449 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.449 | |
| 2y6o | 1N1 | Ephrin type-A receptor 4 | 2.7.10.1 | 0.449 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.449 | |
| 4l0q | NAD | Alcohol dehydrogenase class-3 | / | 0.449 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.448 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 4jld | ADP | Adenylate kinase | / | 0.448 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.447 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.447 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.446 | |
| 2nu9 | COA | Succinate--CoA ligase [ADP-forming] subunit alpha | 6.2.1.5 | 0.446 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.446 | |
| 4kip | 1R9 | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.445 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.445 | |
| 3hx4 | ANP | Calmodulin-domain protein kinase 1 | / | 0.445 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.445 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1osv | CHC | Bile acid receptor | / | 0.444 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2b4r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.444 | |
| 2pe2 | 464 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.444 | |
| 2v2q | NVG | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.444 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.444 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.443 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.443 | |
| 1tvr | TB9 | Gag-Pol polyprotein | 2.7.7.49 | 0.443 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.443 | |
| 2q46 | NAP | Uncharacterized protein At5g02240 | / | 0.443 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.443 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.443 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.443 | |
| 4g3r | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.442 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.442 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 2ag1 | TPP | Benzaldehyde lyase | / | 0.442 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.442 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.442 | |
| 3vw6 | IM6 | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.442 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.442 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.441 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.441 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.441 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.441 | |
| 3wrl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 4l4a | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 4o2b | LOC | Tubulin beta-2B chain | / | 0.441 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.441 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 2x8i | X8I | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.440 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.440 | |
| 3mt8 | 17T | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.440 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.440 | |
| 4mwh | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.440 |