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 |
|---|---|---|---|
| 2d1n | FA4 | Collagenase 3 | 3.4.24 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 1.000 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.611 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.610 | |
| 3o2x | 3O2 | Collagenase 3 | 3.4.24 | 0.586 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.574 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.572 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.567 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.554 | |
| 4a7b | 3W5 | Collagenase 3 | 3.4.24 | 0.545 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.540 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.537 | |
| 2yig | 5EL | Collagenase 3 | 3.4.24 | 0.531 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.531 | |
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 0.525 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.522 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.519 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.516 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.514 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.511 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.509 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.506 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.506 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.502 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.498 | |
| 3kek | 3EK | Collagenase 3 | 3.4.24 | 0.497 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.497 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.496 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.490 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.490 | |
| 3kej | 3EJ | Collagenase 3 | 3.4.24 | 0.489 | |
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 0.487 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.487 | |
| 1xur | PB5 | Collagenase 3 | 3.4.24 | 0.485 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.485 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.483 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.481 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.481 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.481 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.480 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.479 | |
| 3ts4 | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.479 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.478 | |
| 4gql | R47 | Macrophage metalloelastase | 3.4.24.65 | 0.476 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.475 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.472 | |
| 1b3d | S27 | Stromelysin-1 | 3.4.24.17 | 0.471 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.470 | |
| 2f3f | AXF | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 2ow2 | 8MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.469 | |
| 2w0d | CGS | Macrophage metalloelastase | 3.4.24.65 | 0.469 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.461 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.460 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.459 | |
| 1d8m | BBH | Stromelysin-1 | 3.4.24.17 | 0.459 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.458 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.457 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.457 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.456 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.456 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.455 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.455 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.455 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.455 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.453 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.452 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.451 | |
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 | 0.450 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 2r5n | TPP | Transketolase 1 | / | 0.450 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 2ow9 | SP6 | Collagenase 3 | 3.4.24 | 0.449 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.449 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.448 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.448 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.448 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.448 | |
| 5bsf | NAD | Pyrroline-5-carboxylate reductase | / | 0.448 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.447 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3rim | TPP | Transketolase | 2.2.1.1 | 0.447 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4fsl | 0VB | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3k5f | AYH | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.445 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.445 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2yph | QQY | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.445 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.444 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.443 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3k5d | XLI | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.442 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.441 | |
| 1d5j | MM3 | Stromelysin-1 | 3.4.24.17 | 0.441 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.441 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.441 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.441 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.440 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.440 | |
| 4e2y | JHZ | Methyltransferase | / | 0.440 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.440 |