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 |
|---|---|---|---|
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 1.000 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.669 | |
| 3ts4 | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.645 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.604 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.572 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.572 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.571 | |
| 4gql | R47 | Macrophage metalloelastase | 3.4.24.65 | 0.563 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.557 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.556 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.555 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.554 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.548 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.548 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.533 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.531 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.528 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.527 | |
| 3kej | 3EJ | Collagenase 3 | 3.4.24 | 0.527 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.527 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.526 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.521 | |
| 2yig | 5EL | Collagenase 3 | 3.4.24 | 0.521 | |
| 3o2x | 3O2 | Collagenase 3 | 3.4.24 | 0.518 | |
| 4a7b | 3W5 | Collagenase 3 | 3.4.24 | 0.517 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.513 | |
| 3kek | 3EK | Collagenase 3 | 3.4.24 | 0.509 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.508 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.507 | |
| 2ow9 | SP6 | Collagenase 3 | 3.4.24 | 0.502 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.498 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.497 | |
| 1xuc | PB3 | Collagenase 3 | 3.4.24 | 0.493 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.491 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.488 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.483 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.482 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.479 | |
| 1xur | PB5 | Collagenase 3 | 3.4.24 | 0.475 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.473 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.466 | |
| 5dcy | NAP | Iridoid synthase | 1.3.1.99 | 0.465 | |
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 0.464 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.461 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 2ozr | GG1 | Collagenase 3 | 3.4.24 | 0.459 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.459 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.458 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.451 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.451 | |
| 4xgi | NAD | Glutamate dehydrogenase | / | 0.451 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.451 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.450 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.449 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.449 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.449 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.448 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.448 | |
| 1d4d | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.447 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.447 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.447 | |
| 5doz | NDP | JamJ | / | 0.447 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.447 | |
| 3k5d | XLI | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3slz | 3TL | Putative gag-pro-pol polyprotein | / | 0.445 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.444 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.443 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.443 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.443 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.442 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.441 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.441 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.441 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.441 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.440 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.440 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.440 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 |