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 |
|---|---|---|---|
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 1.000 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.574 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.522 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.491 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.475 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.474 | |
| 1jmh | UMP | Thymidylate synthase | / | 0.472 | |
| 2ztu | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.472 | |
| 4l4x | NDP | AmphI | / | 0.472 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.470 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.470 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.469 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.468 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.468 | |
| 1kfb | IGP | Tryptophan synthase alpha chain | / | 0.466 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.464 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.463 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.463 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.462 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.461 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.459 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.459 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.459 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.458 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.458 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.458 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.458 | |
| 2b36 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 3gob | HXX | DdmC | / | 0.457 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.456 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.456 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.455 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.455 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.455 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.454 | |
| 2fr1 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.454 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.454 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.454 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.453 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.453 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.453 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 1fml | RTL | Retinol dehydratase | / | 0.452 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.452 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 2i3g | NAP | N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | 0.451 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.451 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.451 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.450 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.450 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.449 | |
| 2p3b | 3TL | V-1 protease | / | 0.449 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.449 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.449 | |
| 3mtw | M3R | Xaa-Pro dipeptidase, putative | / | 0.449 | |
| 5by6 | UMP | Thymidylate synthase | / | 0.449 | |
| 2qn3 | F55 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.448 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.448 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.448 | |
| 1gpd | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.447 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1qr6 | NAD | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.447 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.447 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.447 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.447 | |
| 1bid | UMP | Thymidylate synthase | / | 0.446 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.446 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.445 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.445 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.445 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.445 | |
| 1omo | NAD | Alanine dehydrogenase | / | 0.444 | |
| 4a6r | TA8 | Probable aminotransferase | / | 0.444 | |
| 4iq7 | 1G9 | Mycocyclosin synthase | 1.14.21.9 | 0.444 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.444 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.443 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.443 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.443 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.443 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.443 | |
| 4hxy | NDP | Plm1 | / | 0.443 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.442 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.442 | |
| 1eno | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic | 1.3.1.9 | 0.442 | |
| 1qyx | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.442 | |
| 4fiz | CUE | 17beta-hydroxysteroid dehydrogenase | / | 0.442 | |
| 4h0u | UMP | Thymidylate synthase | / | 0.442 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.442 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2ejz | SAH | Diphthine synthase | / | 0.441 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.441 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.440 | |
| 4qys | PLR | Tryptophan synthase beta chain 2 | 4.2.1.20 | 0.440 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.440 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.440 |