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 |
|---|---|---|---|
| 4pgh | SAM | Caffeic acid O-methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4pgh | SAM | Caffeic acid O-methyltransferase | / | 1.000 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.486 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.482 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.477 | |
| 4fdu | IHS | Putative multiple inositol polyphosphate histidine phosphatase 1 | / | 0.477 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.476 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.464 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.464 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.463 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.463 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.463 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.461 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.461 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.460 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.460 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.460 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.459 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.459 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.458 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.458 | |
| 1p9w | ANP | Type II secretion system protein E | / | 0.457 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.457 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.457 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.456 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.455 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.454 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.454 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.454 | |
| 4ijr | NDP | D-arabinose dehydrogenase [NAD(P)+] heavy chain | 1.1.1.117 | 0.454 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.453 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 2ien | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.451 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.451 | |
| 3lqs | PSZ | D-alanine aminotransferase | 2.6.1.21 | 0.451 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.451 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.450 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.449 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.449 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.449 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.449 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.448 | |
| 2b4r | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.448 | |
| 3k5g | BJC | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.448 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.447 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.447 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.447 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.447 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.447 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.447 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.446 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.446 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.446 | |
| 2voj | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.446 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.446 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.444 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.444 | |
| 3ut5 | LOC | Tubulin beta chain | / | 0.444 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.444 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.443 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.443 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.443 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.442 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.442 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.442 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.441 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.441 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.441 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 3zuy | TCH | Transporter | / | 0.441 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.441 | |
| 5kwv | ANP | Pantothenate synthetase | / | 0.441 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.440 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.440 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 1rek | B8L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.440 | |
| 3bts | NAD | Galactose/lactose metabolism regulatory protein GAL80 | / | 0.440 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4a6b | QG8 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 4eud | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.440 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.440 |