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 |
|---|---|---|---|
| 3i7i | 518 | Collagenase 3 | 3.4.24 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 1.000 | |
| 4a7b | 3W5 | Collagenase 3 | 3.4.24 | 0.725 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.628 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.620 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.609 | |
| 2yig | 5EL | Collagenase 3 | 3.4.24 | 0.609 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.608 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.606 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.605 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.601 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.600 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.595 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.594 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.578 | |
| 3ts4 | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.577 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.574 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.573 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.572 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.571 | |
| 4gql | R47 | Macrophage metalloelastase | 3.4.24.65 | 0.569 | |
| 3kej | 3EJ | Collagenase 3 | 3.4.24 | 0.567 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.566 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.564 | |
| 1xur | PB5 | Collagenase 3 | 3.4.24 | 0.563 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.560 | |
| 1xuc | PB3 | Collagenase 3 | 3.4.24 | 0.560 | |
| 3o2x | 3O2 | Collagenase 3 | 3.4.24 | 0.559 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.558 | |
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 0.557 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.557 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.557 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.553 | |
| 2ow9 | SP6 | Collagenase 3 | 3.4.24 | 0.551 | |
| 3kek | 3EK | Collagenase 3 | 3.4.24 | 0.551 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.551 | |
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 0.544 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.541 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.539 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.538 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.538 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.535 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.534 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.533 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.532 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.530 | |
| 2w0d | CGS | Macrophage metalloelastase | 3.4.24.65 | 0.513 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.512 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.511 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.510 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.508 | |
| 2ozr | GG1 | Collagenase 3 | 3.4.24 | 0.502 | |
| 2ow2 | 8MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.499 | |
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 0.495 | |
| 1hov | I52 | 72 kDa type IV collagenase | 3.4.24.24 | 0.495 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.494 | |
| 1b3d | S27 | Stromelysin-1 | 3.4.24.17 | 0.493 | |
| 2wo9 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.492 | |
| 1d8m | BBH | Stromelysin-1 | 3.4.24.17 | 0.491 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.488 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.480 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.479 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.472 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.470 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.470 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.466 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.466 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.465 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.464 | |
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 | 0.461 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.459 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.457 | |
| 2x8i | X8I | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.457 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.452 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.452 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.452 | |
| 4l4x | NDP | AmphI | / | 0.449 | |
| 1d5j | MM3 | Stromelysin-1 | 3.4.24.17 | 0.448 | |
| 2dgn | DOI | Adenylosuccinate synthetase isozyme 1 | / | 0.446 | |
| 2bhi | SFT | Cytotoxin 3 | / | 0.444 | |
| 2v6g | NAP | 3-oxo-Delta(4,5)-steroid 5-beta-reductase | / | 0.444 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.443 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.440 |