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 |
|---|---|---|---|
| 4zdc | CO8 | 3,2-trans-enoyl-CoA isomerase | 5.3.3.8 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4zdc | CO8 | 3,2-trans-enoyl-CoA isomerase | 5.3.3.8 | 1.000 | |
| 4zdb | CAA | 3,2-trans-enoyl-CoA isomerase | 5.3.3.8 | 0.611 | |
| 3q0g | BCO | Probable enoyl-CoA hydratase echA8 | 4.2.1.17 | 0.501 | |
| 3q0g | COA | Probable enoyl-CoA hydratase echA8 | 4.2.1.17 | 0.486 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.480 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.474 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.473 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.472 | |
| 4wx2 | F6F | Tryptophan synthase alpha chain | / | 0.472 | |
| 4wx2 | F6F | Tryptophan synthase beta chain | 4.2.1.20 | 0.472 | |
| 1r0e | DFN | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.469 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.469 | |
| 2wd9 | IBP | Acyl-coenzyme A synthetase ACSM2A, mitochondrial | 6.2.1.2 | 0.469 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 3l9l | L9L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.468 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.467 | |
| 3mje | NDP | AmphB | / | 0.467 | |
| 2w6q | OA5 | Biotin carboxylase | 6.3.4.14 | 0.466 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.464 | |
| 1gaq | FAD | Ferredoxin | / | 0.464 | |
| 1i59 | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.464 | |
| 1dub | CAA | Enoyl-CoA hydratase, mitochondrial | 4.2.1.17 | 0.463 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.463 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.462 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.461 | |
| 3dtc | VIN | Mitogen-activated protein kinase kinase kinase 9 | 2.7.11.25 | 0.461 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.460 | |
| 4eji | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.460 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 3glu | LYS_VAL_MET | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.458 | |
| 3ivc | FG4 | Pantothenate synthetase | 6.3.2.1 | 0.458 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 1p7t | ACO | Malate synthase G | / | 0.456 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.456 | |
| 3b7d | CNI | Glutamate receptor 2 | / | 0.455 | |
| 3w5u | FAD | Ferredoxin | / | 0.455 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.454 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.453 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.453 | |
| 6std | MS2 | Scytalone dehydratase | 4.2.1.94 | 0.453 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.452 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.452 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.451 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.451 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.451 | |
| 1mj3 | HXC | Enoyl-CoA hydratase, mitochondrial | 4.2.1.17 | 0.450 | |
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 | 0.450 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.450 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.450 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.450 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.449 | |
| 1tkb | N1T | Transketolase 1 | 2.2.1.1 | 0.449 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.449 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.448 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.448 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 3bnk | FMN | Flavoredoxin | / | 0.448 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.447 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3tlj | SAH | Uncharacterized protein | / | 0.447 | |
| 4b67 | FAD | L-ornithine N(5)-monooxygenase | / | 0.447 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.447 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.447 | |
| 1ozq | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.445 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.445 | |
| 3bfb | 9OD | Pheromone-binding protein ASP1 | / | 0.445 | |
| 3mhp | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.445 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.445 | |
| 3ipq | 965 | Oxysterols receptor LXR-alpha | / | 0.444 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.444 | |
| 4rrm | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.444 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.444 | |
| 5cp8 | TCU | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 1fml | RTL | Retinol dehydratase | / | 0.443 | |
| 1m9j | CLW | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.443 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.443 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.443 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.443 | |
| 4b67 | NAP | L-ornithine N(5)-monooxygenase | / | 0.443 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.443 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 4iwv | 1J9 | Glucokinase | 2.7.1.2 | 0.442 | |
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.442 | |
| 1aqu | EST | Estrogen sulfotransferase, testis isoform | 2.8.2.4 | 0.441 | |
| 1gaw | FAD | Ferredoxin | / | 0.441 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1pq6 | 965 | Oxysterols receptor LXR-beta | / | 0.441 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.441 | |
| 3hzi | ATP | Serine/threonine-protein kinase toxin HipA | / | 0.441 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.441 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.441 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.440 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.440 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.440 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 3f90 | FMN | Flavodoxin | / | 0.440 | |
| 3h1v | TK1 | Glucokinase | 2.7.1.2 | 0.440 | |
| 3sp9 | IL2 | Peroxisome proliferator-activated receptor delta | / | 0.440 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.440 | |
| 4eh8 | IRG | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.440 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.440 | |
| 4zqc | F6F | Tryptophan synthase alpha chain | / | 0.440 |