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 |
|---|---|---|---|
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 1.000 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.562 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.559 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.542 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.542 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.539 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.537 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.527 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.525 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.522 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.521 | |
| 4a7b | 3W5 | Collagenase 3 | 3.4.24 | 0.521 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.518 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.516 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.513 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.512 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.506 | |
| 4gql | R47 | Macrophage metalloelastase | 3.4.24.65 | 0.506 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.506 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.505 | |
| 3o2x | 3O2 | Collagenase 3 | 3.4.24 | 0.504 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.500 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.499 | |
| 3ts4 | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.498 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.491 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.488 | |
| 3kej | 3EJ | Collagenase 3 | 3.4.24 | 0.485 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.482 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.481 | |
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 0.481 | |
| 2v6g | NAP | 3-oxo-Delta(4,5)-steroid 5-beta-reductase | / | 0.476 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.474 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.472 | |
| 4irn | FAD | AnaB | / | 0.472 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 2yig | 5EL | Collagenase 3 | 3.4.24 | 0.470 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.468 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.466 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.463 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 4fco | 0U4 | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.461 | |
| 5dcy | NAP | Iridoid synthase | 1.3.1.99 | 0.460 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.459 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.456 | |
| 2z2d | HSI | Macrophage metalloelastase | 3.4.24.65 | 0.456 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.456 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.454 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.452 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.452 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.451 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3wsw | NAD | L-lactate dehydrogenase | / | 0.451 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.450 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.450 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.449 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.449 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.449 | |
| 3up0 | D7S | aceDAF-12 | / | 0.449 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.449 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.448 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.448 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.448 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.446 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4isk | 1JY | Thymidylate synthase | / | 0.446 | |
| 1xur | PB5 | Collagenase 3 | 3.4.24 | 0.445 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.445 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.445 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4iv6 | FDA | Isovaleryl-CoA dehydrogenase | / | 0.445 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.444 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.444 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.442 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.442 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.442 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.442 | |
| 4h1q | 0XX | Matrix metalloproteinase-9 | 3.4.24.35 | 0.442 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.441 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.441 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.440 |