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 |
|---|---|---|---|
| 3tfy | MET_LEU_GLY_PRO | N-alpha-acetyltransferase 50 | 2.3.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3tfy | MET_LEU_GLY_PRO | N-alpha-acetyltransferase 50 | 2.3.1 | 1.000 | |
| 3tfy | COA | N-alpha-acetyltransferase 50 | 2.3.1 | 0.545 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.494 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.483 | |
| 3up0 | D7S | aceDAF-12 | / | 0.482 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.481 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.481 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.474 | |
| 1k4m | NAD | Nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.473 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.472 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.471 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.471 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.471 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.468 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.467 | |
| 4l4x | NDP | AmphI | / | 0.463 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.462 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.461 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.461 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.460 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.460 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.459 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.459 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.458 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.458 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.458 | |
| 1osv | CHC | Bile acid receptor | / | 0.456 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4n3r | 2GU | Tankyrase-1 | 2.4.2.30 | 0.456 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.455 | |
| 2e7r | SAH | Diphthine synthase | / | 0.454 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.454 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.454 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.453 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.452 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.451 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.451 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.451 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.451 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.451 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.450 | |
| 3bxx | QUE | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.450 | |
| 5epo | TUD | 7-alpha-hydroxysteroid deydrogenase | / | 0.450 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.450 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.449 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.449 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.449 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.449 | |
| 2eeq | SAH | Diphthine synthase | / | 0.448 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.448 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.448 | |
| 3vuc | HHE | Renin | 3.4.23.15 | 0.448 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.447 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.447 | |
| 2dsi | SAH | Diphthine synthase | / | 0.447 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.447 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.447 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.446 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3e6e | DCS | Alanine racemase | / | 0.446 | |
| 3ndj | JHZ | Methyltransferase | / | 0.446 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.446 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.446 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.446 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.445 | |
| 2r9w | 23C | Beta-lactamase | 3.5.2.6 | 0.444 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1e1c | DCA | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.443 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.443 | |
| 2dsh | SAH | Diphthine synthase | / | 0.443 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.443 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.443 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 1opm | IYG | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.441 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.441 | |
| 2ejz | SAH | Diphthine synthase | / | 0.441 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.441 | |
| 2vj6 | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.440 | |
| 2irz | I02 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 |