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 |
|---|---|---|---|
| 2vj9 | VG7 | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2vj9 | VG7 | Beta-secretase 1 | 3.4.23.46 | 1.000 | |
| 2viz | VG4 | Beta-secretase 1 | 3.4.23.46 | 0.726 | |
| 2vj7 | VG6 | Beta-secretase 1 | 3.4.23.46 | 0.695 | |
| 2xfj | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.621 | |
| 2xfk | AA9 | Beta-secretase 1 | 3.4.23.46 | 0.606 | |
| 2ph8 | 35A | Beta-secretase 1 | 3.4.23.46 | 0.565 | |
| 2xfi | XFI | Beta-secretase 1 | 3.4.23.46 | 0.555 | |
| 2b8v | 3BN | Beta-secretase 1 | 3.4.23.46 | 0.532 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.526 | |
| 3i25 | MV7 | Beta-secretase 1 | 3.4.23.46 | 0.525 | |
| 2vnm | CM8 | Beta-secretase 1 | 3.4.23.46 | 0.503 | |
| 2p8h | MY9 | Beta-secretase 1 | 3.4.23.46 | 0.497 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.491 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.491 | |
| 2irz | I02 | Beta-secretase 1 | 3.4.23.46 | 0.486 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.477 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.471 | |
| 4b72 | 2FB | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 2vie | VG0 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.463 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.462 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.461 | |
| 3qi1 | C6A | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.451 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.450 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.449 | |
| 1udb | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.447 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.447 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.447 | |
| 1bdu | DUR | Thymidylate synthase | / | 0.445 | |
| 1bid | UMP | Thymidylate synthase | / | 0.445 | |
| 1c9k | 5GP | Bifunctional adenosylcobalamin biosynthesis protein CobU | / | 0.445 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.445 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.445 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.445 | |
| 1q6t | 600 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.444 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.443 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.443 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.442 | |
| 3k5f | AYH | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.442 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 2rhg | IGP | Tryptophan synthase alpha chain | / | 0.441 | |
| 3toh | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.441 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.440 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.440 |