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 |
|---|---|---|---|
| 1ur5 | NAD | Malate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1ur5 | NAD | Malate dehydrogenase | / | 1.000 | |
| 1guy | NAD | Malate dehydrogenase | / | 0.757 | |
| 1uxk | NAD | Malate dehydrogenase | / | 0.601 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.578 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.556 | |
| 3gvi | ADP | Malate dehydrogenase | / | 0.553 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.552 | |
| 4uun | NAI | L-lactate dehydrogenase | / | 0.530 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.520 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.519 | |
| 1wze | NAD | Malate dehydrogenase | / | 0.507 | |
| 1b8v | NAD | Malate dehydrogenase | / | 0.501 | |
| 1bmd | NAD | Malate dehydrogenase | / | 0.500 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.498 | |
| 2ldb | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.496 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.493 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.491 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.484 | |
| 4i9n | 1E5 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.482 | |
| 1ez4 | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.480 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.480 | |
| 1b8u | NAD | Malate dehydrogenase | / | 0.479 | |
| 1bdm | NAX | Malate dehydrogenase | / | 0.477 | |
| 3wsw | NAD | L-lactate dehydrogenase | / | 0.476 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.475 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.473 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.473 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.473 | |
| 2dc1 | NAD | Probable L-aspartate dehydrogenase | / | 0.471 | |
| 4l4x | NDP | AmphI | / | 0.471 | |
| 4l4s | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.470 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.467 | |
| 1wzi | NDP | Malate dehydrogenase | / | 0.464 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.461 | |
| 1f0x | FAD | D-lactate dehydrogenase | 1.1.1.28 | 0.460 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.460 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.458 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.457 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.456 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.456 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.456 | |
| 2cvq | NDP | Malate dehydrogenase | / | 0.455 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.454 | |
| 3e8x | NAP | BH1520 protein | / | 0.454 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.453 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.453 | |
| 4i9h | 1E4 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.453 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.453 | |
| 1hyh | NAD | L-2-hydroxyisocaproate dehydrogenase | / | 0.452 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.452 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.452 | |
| 1u4o | NDD | L-lactate dehydrogenase | 1.1.1.27 | 0.451 | |
| 1y7t | NDP | Malate dehydrogenase | / | 0.450 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.450 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.449 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.447 | |
| 3anl | SYC | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.447 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.447 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.446 | |
| 1ra8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2jcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.446 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4rls | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.446 | |
| 1emd | NAD | Malate dehydrogenase | / | 0.445 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.445 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.445 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.443 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.443 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.443 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.443 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.443 | |
| 1ra3 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2ge3 | ACO | Probable acetyltransferase | / | 0.442 | |
| 3dck | KVI | Protease | / | 0.442 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3ut5 | LOC | Tubulin beta chain | / | 0.442 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.442 | |
| 2xaa | NAD | Secondary alcohol dehydrogenase | / | 0.441 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.441 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.441 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.440 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.440 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.440 | |
| 5c77 | SAH | Protein arginine N-methyltransferase SFM1 | / | 0.440 |