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 |
|---|---|---|---|
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 1.000 | |
| 4ock | ANP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.721 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.616 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.602 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.558 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.484 | |
| 3nw3 | MU2 | Peptidoglycan recognition protein 1 | / | 0.479 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.478 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.465 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.463 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.461 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.460 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.459 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.458 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.458 | |
| 1hzj | UD1 | UDP-glucose 4-epimerase | / | 0.457 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.457 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.456 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.456 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.455 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.454 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.454 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.454 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.454 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.454 | |
| 4dx7 | DM2 | Multidrug efflux pump subunit AcrB | / | 0.453 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.452 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.452 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.452 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.452 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 2xfy | ACX | Beta-amylase | 3.2.1.2 | 0.451 | |
| 2xx9 | 1NF | Glutamate receptor 2 | / | 0.451 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.451 | |
| 5a3b | APR | SIR2 family protein | / | 0.451 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.450 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.449 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1rj6 | AZM | Carbonic anhydrase 14 | 4.2.1.1 | 0.448 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.448 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.448 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.447 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.447 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.447 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.447 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.447 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.447 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.447 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.446 | |
| 2j07 | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.446 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.446 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4mwh | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.446 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1f4e | TPR | Thymidylate synthase | / | 0.445 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.445 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.445 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.445 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.444 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.444 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.444 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 4fgr | ADP | Phosphoribosylaminoimidazole-succinocarboxamide synthase | 6.3.2.6 | 0.444 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.444 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.443 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.443 | |
| 4jr7 | GNP | Casein kinase II subunit alpha | 2.7.11.1 | 0.443 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.442 | |
| 4gj3 | 0XP | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.442 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.442 | |
| 4lfi | GNP | Casein kinase II subunit alpha | 2.7.11.1 | 0.442 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.441 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.441 | |
| 3h86 | AP5 | Adenylate kinase | / | 0.441 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.441 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.441 | |
| 2d1c | NAP | Isocitrate dehydrogenase [NADP] | 1.1.1.42 | 0.440 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.440 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.440 | |
| 4fi1 | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.440 |