sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4twl | ASC | Dioscorin 5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4twl | ASC | Dioscorin 5 | / | 1.000 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.491 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.490 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.485 | |
| 1woo | THG | Aminomethyltransferase | / | 0.474 | |
| 3u8f | FGM | Ribosome inactivating protein | / | 0.471 | |
| 1wop | FFO | Aminomethyltransferase | / | 0.470 | |
| 4mvc | CDC | Choline-phosphate cytidylyltransferase A | / | 0.468 | |
| 4jt8 | 1NR | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.467 | |
| 4b67 | NAP | L-ornithine N(5)-monooxygenase | / | 0.466 | |
| 4b64 | NAP | L-ornithine N(5)-monooxygenase | / | 0.465 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.464 | |
| 4b65 | NDP | L-ornithine N(5)-monooxygenase | / | 0.464 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 1b9i | PXG | 3-amino-5-hydroxybenzoate synthase | 4.2.1.144 | 0.460 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.460 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.459 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.459 | |
| 1akb | PPD | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.458 | |
| 3c1o | NAP | Eugenol synthase | / | 0.457 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 4bqy | FNT | Egl nine homolog 1 | / | 0.456 | |
| 5ilw | URI | Ribosome inactivating protein | / | 0.456 | |
| 2re8 | GSU | Glutamine--tRNA ligase | 6.1.1.18 | 0.454 | |
| 3upk | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.454 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.454 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.453 | |
| 3dd1 | 25D | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.452 | |
| 5jdz | SAH | Methyl transferase | / | 0.451 | |
| 3ghh | 2NF | CD38 molecule | / | 0.450 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.450 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.450 | |
| 1euy | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.449 | |
| 1hlk | 113 | Metallo-beta-lactamase type 2 | / | 0.449 | |
| 2zvc | SAH | Precorrin-3 C17-methyltransferase | / | 0.449 | |
| 3h23 | B54 | Dihydropteroate synthase | / | 0.449 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.449 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.449 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2qcx | PF1 | Aminopyrimidine aminohydrolase | / | 0.448 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.447 | |
| 3arv | SAU | Chitinase A | / | 0.447 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.447 | |
| 4iif | CTS | Beta-glucosidase 1 | 3.2.1.21 | 0.447 | |
| 4ivr | N50 | Thymidine kinase | / | 0.447 | |
| 4ku7 | PCG | cGMP-dependent protein kinase 1 | 2.7.11.12 | 0.447 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.446 | |
| 4lwx | MU2 | Ribosome inactivating protein | / | 0.446 | |
| 4s1i | PLP | Pyridoxal kinase, putative | / | 0.446 | |
| 5fsi | 8DG | 7,8-dihydro-8-oxoguanine triphosphatase | 3.6.1.55 | 0.446 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.445 | |
| 1toj | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.445 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.445 | |
| 4jbx | SK7 | Thymidine kinase | / | 0.445 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.444 | |
| 2cft | PLP | Pyridoxal phosphate phosphatase | / | 0.444 | |
| 4jt9 | 1NS | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.444 | |
| 1e2n | RCA | Thymidine kinase | / | 0.443 | |
| 1og1 | TAD | T-cell ecto-ADP-ribosyltransferase 2 | / | 0.443 | |
| 1tou | B1V | Fatty acid-binding protein, adipocyte | / | 0.443 | |
| 3zgz | 84T | Leucine--tRNA ligase | / | 0.443 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.443 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.442 | |
| 1pl6 | 572 | Sorbitol dehydrogenase | 1.1.1.14 | 0.442 | |
| 2gms | P0P | Putative pyridoxamine 5-phosphate-dependent dehydrase | / | 0.442 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.442 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.442 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.442 | |
| 4h0v | NAD | Iota toxin component Ia | / | 0.442 | |
| 1qrs | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.441 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.441 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.441 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.441 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.441 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.441 | |
| 4bqw | QNM | Egl nine homolog 1 | / | 0.441 | |
| 4k88 | HFG | Bifunctional glutamate/proline--tRNA ligase | 6.1.1.15 | 0.441 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2vcx | D26 | Hematopoietic prostaglandin D synthase | / | 0.440 | |
| 2yyu | C5P | Orotidine 5'-phosphate decarboxylase | / | 0.440 | |
| 3phj | DHK | Shikimate dehydrogenase (NADP(+)) | / | 0.440 |