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 |
|---|---|---|---|
| 2y6d | TQJ | Matrilysin | 3.4.24.23 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2y6d | TQJ | Matrilysin | 3.4.24.23 | 1.000 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.541 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.510 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.506 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.504 | |
| 1b3d | S27 | Stromelysin-1 | 3.4.24.17 | 0.503 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.496 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.496 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.493 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.488 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.488 | |
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 0.487 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.486 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.485 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.484 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.483 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.480 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.479 | |
| 1d8m | BBH | Stromelysin-1 | 3.4.24.17 | 0.478 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.478 | |
| 4gql | R47 | Macrophage metalloelastase | 3.4.24.65 | 0.478 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.477 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.477 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.476 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.473 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.472 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.471 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.468 | |
| 1xur | PB5 | Collagenase 3 | 3.4.24 | 0.466 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.465 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.465 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.464 | |
| 3ts4 | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.464 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.463 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.462 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.462 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.461 | |
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 0.459 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.459 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.459 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.456 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.455 | |
| 4a7b | 3W5 | Collagenase 3 | 3.4.24 | 0.454 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.452 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.452 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.451 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.451 | |
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 0.449 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.449 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.449 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.445 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.445 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.445 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.445 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.444 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.443 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.443 | |
| 2ejz | SAH | Diphthine synthase | / | 0.443 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.443 | |
| 3x1d | GDP | Atlastin | 3.6.5 | 0.443 | |
| 3kej | 3EJ | Collagenase 3 | 3.4.24 | 0.442 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4h30 | 0ZD | Macrophage metalloelastase | 3.4.24.65 | 0.442 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.442 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.442 | |
| 5ab6 | CAA | Nonspecific lipid-transfer protein, putative | / | 0.442 | |
| 5ab7 | MLC | Nonspecific lipid-transfer protein, putative | / | 0.442 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.441 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.441 |