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 |
|---|---|---|---|
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 1.000 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.623 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.619 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.616 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.614 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.612 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.611 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.603 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.601 | |
| 4a7b | 3W5 | Collagenase 3 | 3.4.24 | 0.601 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.597 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.596 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.593 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.590 | |
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 0.589 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.584 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.583 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.583 | |
| 1xur | PB5 | Collagenase 3 | 3.4.24 | 0.582 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.581 | |
| 3kej | 3EJ | Collagenase 3 | 3.4.24 | 0.576 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.575 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.575 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.575 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.572 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.572 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.571 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.571 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.571 | |
| 3kek | 3EK | Collagenase 3 | 3.4.24 | 0.568 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.566 | |
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 | 0.566 | |
| 3ts4 | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.566 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.565 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.564 | |
| 2w0d | CGS | Macrophage metalloelastase | 3.4.24.65 | 0.563 | |
| 1b3d | S27 | Stromelysin-1 | 3.4.24.17 | 0.562 | |
| 2yig | 5EL | Collagenase 3 | 3.4.24 | 0.559 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.559 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.559 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.557 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.556 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.551 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.549 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.547 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.545 | |
| 2ow2 | 8MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.545 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.542 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.541 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.539 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.537 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.535 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.535 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.533 | |
| 4gql | R47 | Macrophage metalloelastase | 3.4.24.65 | 0.533 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.532 | |
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 0.530 | |
| 3o2x | 3O2 | Collagenase 3 | 3.4.24 | 0.530 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.528 | |
| 2ow9 | SP6 | Collagenase 3 | 3.4.24 | 0.528 | |
| 1hov | I52 | 72 kDa type IV collagenase | 3.4.24.24 | 0.519 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.519 | |
| 1d8m | BBH | Stromelysin-1 | 3.4.24.17 | 0.515 | |
| 2wo9 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.515 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.514 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.510 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.508 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.499 | |
| 4h49 | L29 | Macrophage metalloelastase | 3.4.24.65 | 0.493 | |
| 2y6d | TQJ | Matrilysin | 3.4.24.23 | 0.486 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.484 | |
| 1fm1 | WAY | Collagenase 3 | 3.4.24 | 0.480 | |
| 1rm8 | BAT | Matrix metalloproteinase-16 | 3.4.24 | 0.476 | |
| 2jih | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 1 | 3.4.24 | 0.474 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.471 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 1d5j | MM3 | Stromelysin-1 | 3.4.24.17 | 0.467 | |
| 2oy2 | ILE_ALA_GLY | Neutrophil collagenase | 3.4.24.34 | 0.467 | |
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 | 0.459 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.456 | |
| 4rh1 | 0TT | Spore photoproduct lyase | / | 0.449 | |
| 2e7r | SAH | Diphthine synthase | / | 0.448 | |
| 3q8h | AO9 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.446 | |
| 3zbz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.446 | |
| 4o4f | ATP | Kinase | / | 0.445 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.445 | |
| 1atl | 0QI | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.444 | |
| 1dth | BAT | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.444 | |
| 2eeq | SAH | Diphthine synthase | / | 0.444 | |
| 2dsh | SAH | Diphthine synthase | / | 0.443 | |
| 2dsi | SAH | Diphthine synthase | / | 0.443 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.443 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.442 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.441 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 1rbz | KT5 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.440 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.440 | |
| 3fqk | 79Z | Genome polyprotein | 2.7.7.48 | 0.440 |