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 |
|---|---|---|---|
| 1o94 | ADP | Trimethylamine dehydrogenase | 1.5.8.2 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1o94 | ADP | Trimethylamine dehydrogenase | 1.5.8.2 | 1.000 | |
| 1djq | ADP | Trimethylamine dehydrogenase | 1.5.8.2 | 0.661 | |
| 2tmd | ADP | Trimethylamine dehydrogenase | 1.5.8.2 | 0.659 | |
| 1djn | ADP | Trimethylamine dehydrogenase | 1.5.8.2 | 0.657 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.528 | |
| 1u7h | NAD | Putative ornithine cyclodeaminase | / | 0.521 | |
| 1w4x | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.516 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.512 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.511 | |
| 2yls | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.501 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.496 | |
| 3cge | FAD | Coenzyme A disulfide reductase | / | 0.490 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.490 | |
| 2gr2 | APR | Ferredoxin reductase | / | 0.488 | |
| 2gr0 | ADP | Ferredoxin reductase | / | 0.484 | |
| 4u8i | FDA | UDP-galactopyranose mutase | / | 0.483 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.481 | |
| 3gon | ANP | Phosphomevalonate kinase | / | 0.481 | |
| 1x7d | NAD | Putative ornithine cyclodeaminase | / | 0.480 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.479 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.478 | |
| 2ylx | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.477 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.477 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.476 | |
| 3uox | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.475 | |
| 3djg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.474 | |
| 1ges | FAD | Glutathione reductase | 1.8.1.7 | 0.473 | |
| 2uzw | SS4 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.473 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.473 | |
| 4bk3 | FAD | Probable salicylate monooxygenase | / | 0.468 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.467 | |
| 2rab | FAD | Glutathione amide reductase | / | 0.465 | |
| 4b69 | FAD | L-ornithine N(5)-monooxygenase | / | 0.464 | |
| 4y9q | C2E | Uncharacterized protein | / | 0.464 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.463 | |
| 4dsg | FAD | Uncharacterized protein | / | 0.463 | |
| 1ydr | IQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.462 | |
| 2zzc | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.461 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.460 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.459 | |
| 1geu | FAD | Glutathione reductase | 1.8.1.7 | 0.458 | |
| 2yr5 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.458 | |
| 3vqh | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.458 | |
| 1j1z | ATP | Argininosuccinate synthase | / | 0.457 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.456 | |
| 3k30 | ADP | Histamine dehydrogenase | / | 0.456 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.455 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.455 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.455 | |
| 5br7 | FAD | UDP-galactopyranose mutase | / | 0.455 | |
| 1e1l | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.454 | |
| 3gwd | FAD | Cyclohexanone monooxygenase | / | 0.454 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.454 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4x9n | FAD | Uncharacterized protein MG039 homolog | / | 0.454 | |
| 2vhx | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.453 | |
| 3dgh | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.453 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.453 | |
| 4s26 | SAH | Phosphomethylpyrimidine synthase, chloroplastic | 4.1.99.17 | 0.453 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.452 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.452 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.452 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.451 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.451 | |
| 3ely | SAH | Methyltransferase | / | 0.451 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.450 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.450 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.450 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.449 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 2cvj | FAD | Thioredoxin reductase related protein | / | 0.448 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.447 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.447 | |
| 3qv1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.447 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.447 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.446 | |
| 2xrl | DXT | Tetracycline repressor protein class D | / | 0.446 | |
| 1q8u | H52 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.445 | |
| 3nn6 | FB0 | 6-hydroxy-L-nicotine oxidase | / | 0.444 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.444 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.444 | |
| 2b4y | APR | NAD-dependent protein deacylase sirtuin-5, mitochondrial | / | 0.443 | |
| 2q0l | FAD | Thioredoxin reductase | 1.8.1.9 | 0.443 | |
| 3fg2 | FAD | Putative rubredoxin reductase | / | 0.443 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.443 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.443 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1get | FAD | Glutathione reductase | 1.8.1.7 | 0.442 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.442 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.442 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.442 | |
| 2amt | 1AA | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.441 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.441 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3ivc | FG4 | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 1esq | TZP | Hydroxyethylthiazole kinase | / | 0.440 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.440 | |
| 2vo6 | M05 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 3dzv | ADP | Hydroxyethylthiazole kinase | / | 0.440 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 4d9m | 0JO | Diaminopropionate ammonia-lyase | 4.3.1.15 | 0.440 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.440 |