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 |
|---|---|---|---|
| 2d1n | FA4 | Collagenase 3 | 3.4.24 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 1.000 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.610 | |
| 3o2x | 3O2 | Collagenase 3 | 3.4.24 | 0.591 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.569 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.553 | |
| 4a7b | 3W5 | Collagenase 3 | 3.4.24 | 0.546 | |
| 2yig | 5EL | Collagenase 3 | 3.4.24 | 0.536 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.524 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.514 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.511 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.510 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.509 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.508 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.508 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.503 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.502 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.493 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.489 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.489 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.487 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.485 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.484 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.482 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.482 | |
| 3ts4 | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.479 | |
| 4gql | R47 | Macrophage metalloelastase | 3.4.24.65 | 0.478 | |
| 3kej | 3EJ | Collagenase 3 | 3.4.24 | 0.477 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.475 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.473 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.471 | |
| 2f3f | AXF | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.470 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.468 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.467 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.465 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.462 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 3kek | 3EK | Collagenase 3 | 3.4.24 | 0.460 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.459 | |
| 1xur | PB5 | Collagenase 3 | 3.4.24 | 0.458 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.458 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.458 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.458 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.457 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.456 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.455 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.455 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.454 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.453 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.453 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.453 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3ge6 | FMN | Nitroreductase | / | 0.453 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.452 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4e2y | JHZ | Methyltransferase | / | 0.450 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.447 | |
| 1e3l | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.447 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.447 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.447 | |
| 3k5f | AYH | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2pob | GW4 | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.444 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.444 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.444 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.443 | |
| 3k5d | XLI | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.442 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.442 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.442 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.441 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.441 | |
| 4gid | 0GH | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1k0l | FAD | p-hydroxybenzoate hydroxylase | / | 0.440 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.440 | |
| 2jbs | FMN | p-hydroxyphenylacetate 3-hydroxylase, oxygenase component | / | 0.440 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.440 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.440 |