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 |
|---|---|---|---|
| 4ew2 | DXY | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4ew2 | DXY | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 1.000 | |
| 4ew3 | DXZ | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.634 | |
| 1c2t | NHS | Phosphoribosylglycinamide formyltransferase | / | 0.498 | |
| 1jkx | 138 | Phosphoribosylglycinamide formyltransferase | / | 0.498 | |
| 1rby | GAR | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.485 | |
| 1c2t | GAR | Phosphoribosylglycinamide formyltransferase | / | 0.484 | |
| 1c3e | NHR | Phosphoribosylglycinamide formyltransferase | / | 0.480 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.472 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.470 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.470 | |
| 1rc0 | KT5 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.467 | |
| 1rbz | KT5 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.463 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.463 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.463 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.463 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.463 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.462 | |
| 1cde | DZF | Phosphoribosylglycinamide formyltransferase | / | 0.461 | |
| 1c3e | GAR | Phosphoribosylglycinamide formyltransferase | / | 0.460 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.460 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.460 | |
| 1cde | GAR | Phosphoribosylglycinamide formyltransferase | / | 0.459 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.459 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.458 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.457 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.457 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.457 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.457 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.456 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.456 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.456 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.455 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.454 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.454 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.454 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.454 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.453 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.453 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.453 | |
| 3dv3 | MEK | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.453 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.451 | |
| 1rbq | KEU | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.451 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.451 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.450 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.450 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.449 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.449 | |
| 1eag | A70 | Candidapepsin-2 | 3.4.23.24 | 0.448 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.448 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3da2 | 4MD | Carbonic anhydrase 13 | 4.2.1.1 | 0.447 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.447 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.446 | |
| 3oet | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.446 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.446 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.445 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.445 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.445 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.445 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.445 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.445 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 1men | GAR | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.444 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.444 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.444 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.444 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.444 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4l4x | NDP | AmphI | / | 0.443 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 2yph | QQY | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 4a61 | ANP | Plasmid segregation protein ParM | / | 0.442 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.442 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.441 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1gqt | ACP | Ribokinase | / | 0.440 | |
| 2owf | SAH | Diphthine synthase | / | 0.440 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.440 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.440 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.440 | |
| 4qxq | 1YE | Stimulator of interferon genes protein | / | 0.440 | |
| 5a3b | APR | SIR2 family protein | / | 0.440 |