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 |
|---|---|---|---|
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 | 1.000 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.571 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.556 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.546 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.545 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.538 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.537 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.533 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.530 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.528 | |
| 1dth | BAT | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.523 | |
| 1atl | 0QI | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.521 | |
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 | 0.520 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.518 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.517 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.515 | |
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.513 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.512 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.508 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.507 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.507 | |
| 2xs4 | ALA_PHE_THR | Karilysin | 3.4.24 | 0.505 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.503 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.503 | |
| 2wo9 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.500 | |
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 0.499 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.499 | |
| 2xs3 | ALA_PHE_THR_SER | Karilysin | 3.4.24 | 0.499 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.499 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.496 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.496 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.494 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.488 | |
| 2srt | INH | Stromelysin-1 | 3.4.24.17 | 0.486 | |
| 1d5j | MM3 | Stromelysin-1 | 3.4.24.17 | 0.484 | |
| 2dw0 | GM6 | Zinc metalloproteinase-disintegrin-like VAP2B | 3.4.24 | 0.481 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.478 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.478 | |
| 1rm8 | BAT | Matrix metalloproteinase-16 | 3.4.24 | 0.477 | |
| 3b92 | 440 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.477 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.477 | |
| 3ayk | CGS | Interstitial collagenase | 3.4.24.7 | 0.475 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.475 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.473 | |
| 2w0d | CGS | Macrophage metalloelastase | 3.4.24.65 | 0.472 | |
| 1jk3 | BAT | Macrophage metalloelastase | 3.4.24.65 | 0.470 | |
| 1fm1 | WAY | Collagenase 3 | 3.4.24 | 0.469 | |
| 3kek | 3EK | Collagenase 3 | 3.4.24 | 0.467 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.466 | |
| 3muo | ZPR | Prolyl endopeptidase | / | 0.466 | |
| 1d8m | BBH | Stromelysin-1 | 3.4.24.17 | 0.464 | |
| 2w13 | WR2 | Snake venom metalloproteinase BaP1 | 3.4.24 | 0.461 | |
| 3kmc | 403 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.460 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.458 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.456 | |
| 2oy2 | ILE_ALA_GLY | Neutrophil collagenase | 3.4.24.34 | 0.454 | |
| 2owv | SAH | Diphthine synthase | / | 0.453 | |
| 1fls | WAY | Collagenase 3 | 3.4.24 | 0.452 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.451 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.451 | |
| 4wso | NAD | Probable nicotinate-nucleotide adenylyltransferase | / | 0.451 | |
| 1zxc | IH6 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.449 | |
| 2owf | SAH | Diphthine synthase | / | 0.449 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.449 | |
| 2jnp | NGH | Stromelysin-1 | 3.4.24.17 | 0.448 | |
| 2e08 | SAH | Diphthine synthase | / | 0.447 | |
| 2zdy | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.447 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1gc5 | ADP | ADP-dependent glucokinase | 2.7.1.147 | 0.444 | |
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase | / | 0.444 | |
| 4iz0 | 2BI | Genome polyprotein | 2.7.7.48 | 0.444 | |
| 2r8o | T5X | Transketolase 1 | / | 0.443 | |
| 3q8h | AO9 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.443 | |
| 2e0a | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.442 | |
| 3fqk | 79Z | Genome polyprotein | 2.7.7.48 | 0.442 | |
| 4ih7 | 1ER | Genome polyprotein | 2.7.7.48 | 0.442 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.440 |