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 |
|---|---|---|---|
| 1dth | BAT | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1dth | BAT | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 1.000 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.558 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.550 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.550 | |
| 1atl | 0QI | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.548 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.541 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.537 | |
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.537 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.530 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.524 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.523 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.516 | |
| 4h30 | 0ZD | Macrophage metalloelastase | 3.4.24.65 | 0.515 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.513 | |
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 | 0.508 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.507 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.506 | |
| 2xs3 | ALA_PHE_THR_SER | Karilysin | 3.4.24 | 0.505 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.502 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.500 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.497 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.497 | |
| 2xs4 | ALA_PHE_THR | Karilysin | 3.4.24 | 0.496 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.496 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.495 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.495 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.492 | |
| 2dw0 | GM6 | Zinc metalloproteinase-disintegrin-like VAP2B | 3.4.24 | 0.489 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.486 | |
| 2wo9 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.486 | |
| 1jk3 | BAT | Macrophage metalloelastase | 3.4.24.65 | 0.485 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.485 | |
| 2jih | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 1 | 3.4.24 | 0.482 | |
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 0.477 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.475 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.473 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.471 | |
| 1fm1 | WAY | Collagenase 3 | 3.4.24 | 0.470 | |
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 | 0.469 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 2srt | INH | Stromelysin-1 | 3.4.24.17 | 0.461 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.461 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.458 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.458 | |
| 1rm8 | BAT | Matrix metalloproteinase-16 | 3.4.24 | 0.455 | |
| 3kds | NHX | ATP-dependent zinc metalloprotease FtsH | / | 0.455 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.454 | |
| 2y6d | TQJ | Matrilysin | 3.4.24.23 | 0.451 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.450 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.450 | |
| 3lgp | 50X | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.448 | |
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 0.446 | |
| 1u1i | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.446 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4h1q | 0XX | Matrix metalloproteinase-9 | 3.4.24.35 | 0.446 | |
| 5er0 | FAD | Uncharacterized NAD(FAD)-dependent dehydrogenase | / | 0.446 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.445 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.445 | |
| 2y4g | TIR | TamL | / | 0.444 | |
| 3le9 | 727 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.444 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.444 | |
| 4z54 | GDP | Neuronal-specific septin-3 | / | 0.444 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.442 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.442 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.442 | |
| 4xj3 | GTP | Cyclic GMP-AMP synthase | / | 0.442 | |
| 1d5j | MM3 | Stromelysin-1 | 3.4.24.17 | 0.441 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.441 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.441 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.441 | |
| 5ej8 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.441 | |
| 1fls | WAY | Collagenase 3 | 3.4.24 | 0.440 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 2jnp | NGH | Stromelysin-1 | 3.4.24.17 | 0.440 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.440 | |
| 4wdg | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 |