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 |
|---|---|---|---|
| 3i25 | MV7 | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3i25 | MV7 | Beta-secretase 1 | 3.4.23.46 | 1.000 | |
| 2irz | I02 | Beta-secretase 1 | 3.4.23.46 | 0.611 | |
| 2is0 | I03 | Beta-secretase 1 | 3.4.23.46 | 0.590 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.590 | |
| 2b8v | 3BN | Beta-secretase 1 | 3.4.23.46 | 0.588 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.583 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.583 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.576 | |
| 4gid | 0GH | Beta-secretase 1 | 3.4.23.46 | 0.574 | |
| 2p8h | MY9 | Beta-secretase 1 | 3.4.23.46 | 0.569 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.569 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.567 | |
| 4fco | 0U4 | Beta-secretase 1 | 3.4.23.46 | 0.563 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.537 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.531 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.530 | |
| 2xfi | XFI | Beta-secretase 1 | 3.4.23.46 | 0.525 | |
| 2vj7 | VG6 | Beta-secretase 1 | 3.4.23.46 | 0.524 | |
| 2oah | QIN | Beta-secretase 1 | 3.4.23.46 | 0.520 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.519 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.518 | |
| 2wf0 | ZY0 | Beta-secretase 1 | 3.4.23.46 | 0.515 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.515 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.509 | |
| 2wf2 | ZY2 | Beta-secretase 1 | 3.4.23.46 | 0.504 | |
| 4lxm | 1YU | Beta-secretase 1 | 3.4.23.46 | 0.503 | |
| 2viz | VG4 | Beta-secretase 1 | 3.4.23.46 | 0.499 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.493 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.491 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.490 | |
| 2vnn | CM7 | Beta-secretase 1 | 3.4.23.46 | 0.489 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.489 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.488 | |
| 2vj9 | VG7 | Beta-secretase 1 | 3.4.23.46 | 0.483 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.482 | |
| 2vj6 | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.477 | |
| 1w51 | L01 | Beta-secretase 1 | 3.4.23.46 | 0.475 | |
| 2wez | ZYE | Beta-secretase 1 | 3.4.23.46 | 0.473 | |
| 2ph8 | 35A | Beta-secretase 1 | 3.4.23.46 | 0.472 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.470 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.468 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.468 | |
| 2xfk | AA9 | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 3qbh | QBH | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.461 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.461 | |
| 2vie | VG0 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.459 | |
| 2vnm | CM8 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.457 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.457 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.455 | |
| 2xfj | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.452 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.450 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.450 | |
| 4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.449 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.448 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.448 | |
| 2f3f | AXF | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.447 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.446 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.446 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.446 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.445 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.444 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.444 | |
| 2f3e | AXQ | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.443 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.442 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.441 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.441 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.441 | |
| 3k5d | XLI | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.441 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.440 |