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 |
|---|---|---|---|
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 1.000 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.497 | |
| 4l8u | 9AZ | Serum albumin | / | 0.484 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.479 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.472 | |
| 4l2i | FAD | Electron transfer flavoprotein alpha/beta-subunit | / | 0.469 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.467 | |
| 3r1r | ATP | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.467 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.464 | |
| 1rrm | APR | Lactaldehyde reductase | 1.1.1.77 | 0.462 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.462 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.461 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.461 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.461 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.461 | |
| 4qys | PLR | Tryptophan synthase beta chain 2 | 4.2.1.20 | 0.460 | |
| 2npn | SAM | Putative cobalamin synthesis related protein | / | 0.458 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.458 | |
| 1mjh | ATP | Universal stress protein MJ0577 | / | 0.457 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.456 | |
| 1kt3 | RTL | Retinol-binding protein 4 | / | 0.455 | |
| 2wbd | RO5 | Fructose-1,6-bisphosphatase 1 | 3.1.3.11 | 0.455 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.455 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.455 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.454 | |
| 2xvu | 9DN | Serum albumin | / | 0.454 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.454 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 1t09 | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.452 | |
| 4l4x | NDP | AmphI | / | 0.452 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.450 | |
| 1wuu | ANP | Galactokinase | 2.7.1.6 | 0.450 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.450 | |
| 1hk2 | T44 | Serum albumin | / | 0.449 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.449 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.449 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.449 | |
| 1xq6 | NAP | Uncharacterized protein At5g02240 | / | 0.448 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3a3y | OBN | Sodium/potassium-transporting ATPase subunit alpha | / | 0.448 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.448 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.448 | |
| 3bts | NAD | Galactose/lactose metabolism regulatory protein GAL80 | / | 0.447 | |
| 4m11 | MXM | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.447 | |
| 2jlc | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.446 | |
| 2rg6 | 287 | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 3hdy | FAD | UDP-galactopyranose mutase | / | 0.446 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.446 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.446 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.446 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.446 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.445 | |
| 2tct | CTC | Tetracycline repressor protein class D | / | 0.445 | |
| 4dti | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 1gjv | AGS | [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial | 2.7.11.4 | 0.444 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.444 | |
| 3gyj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.444 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.444 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.444 | |
| 4kuh | CAA | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.444 | |
| 1nqo | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.443 | |
| 2bm9 | SAM | Cephalosporin hydroxylase CmcI | / | 0.443 | |
| 2bsm | BSM | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.443 | |
| 2trt | TAC | Tetracycline repressor protein class D | / | 0.443 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.443 | |
| 1nlm | UD1 | UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase | / | 0.442 | |
| 1osv | CHC | Bile acid receptor | / | 0.442 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.442 | |
| 2ohx | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 3aeb | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.442 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.442 | |
| 4k9n | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.442 | |
| 4xye | NAD | Formate dehydrogenase | / | 0.442 | |
| 5d4u | SAM | Uncharacterized protein MJ0489 | / | 0.442 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.441 | |
| 3l9h | EMQ | Kinesin-like protein KIF11 | / | 0.441 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 4d04 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 4kqw | NAP | Ketol-acid reductoisomerase (NADP(+)) | / | 0.441 | |
| 4pd6 | URI | Nucleoside permease | / | 0.441 | |
| 4qvt | ACO | Acetyltransferase YpeA | 2.3.1 | 0.441 | |
| 1oir | HDY | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3bbt | FMM | Receptor tyrosine-protein kinase erbB-4 | 2.7.10.1 | 0.440 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.440 | |
| 3q3c | NAD | NAD-dependent L-serine dehydrogenase | / | 0.440 | |
| 4do3 | 0LA | Fatty-acid amide hydrolase 1 | 3.5.1.99 | 0.440 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.440 | |
| 4i0a | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.440 |