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 |
|---|---|---|---|
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 1.000 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.654 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.645 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.618 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.609 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.485 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.476 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.471 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.467 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.462 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.459 | |
| 5dp2 | NAP | CurF | / | 0.459 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.458 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.458 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.456 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.456 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.456 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.455 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.455 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.453 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.453 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.452 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.452 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.452 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.452 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.452 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.452 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.450 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.450 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.448 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.448 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.448 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.447 | |
| 4j75 | TYM | Tryptophan--tRNA ligase | / | 0.447 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.446 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 1kce | CB3 | Thymidylate synthase | / | 0.446 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.446 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.446 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.446 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.446 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.445 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 3a3g | DLZ | Lumazine protein | / | 0.445 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.444 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.444 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.443 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3muo | ZPR | Prolyl endopeptidase | / | 0.443 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.443 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.442 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.442 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.442 | |
| 4eji | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.442 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.441 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.441 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.441 | |
| 1c9k | 5GP | Bifunctional adenosylcobalamin biosynthesis protein CobU | / | 0.440 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 4f65 | 0S9 | Fibroblast growth factor receptor 1 | / | 0.440 |