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 |
|---|---|---|---|
| 3gvh | NAD | Malate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3gvh | NAD | Malate dehydrogenase | / | 1.000 | |
| 3gvi | ADP | Malate dehydrogenase | / | 0.622 | |
| 1uxk | NAD | Malate dehydrogenase | / | 0.567 | |
| 1guy | NAD | Malate dehydrogenase | / | 0.552 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.550 | |
| 1ur5 | NAD | Malate dehydrogenase | / | 0.546 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.536 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.521 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.516 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.507 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.506 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.504 | |
| 1ez4 | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.503 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.501 | |
| 3wsw | NAD | L-lactate dehydrogenase | / | 0.490 | |
| 4rls | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.488 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.485 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.484 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.481 | |
| 4l4s | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.481 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.480 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.469 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.467 | |
| 3h3f | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.466 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.462 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.462 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.462 | |
| 4uun | NAI | L-lactate dehydrogenase | / | 0.462 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3ieu | GDP | GTPase Era | / | 0.459 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.459 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.459 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.458 | |
| 1u5a | BIK | L-lactate dehydrogenase | 1.1.1.27 | 0.456 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.456 | |
| 4i9n | 1E5 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.456 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.453 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.451 | |
| 2ldb | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.450 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.450 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.450 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.450 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.450 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.449 | |
| 4i9h | 1E4 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.449 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.447 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.447 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.446 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.445 | |
| 2zvc | SAH | Precorrin-3 C17-methyltransferase | / | 0.445 | |
| 3oet | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.445 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.445 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.445 | |
| 1wze | NAD | Malate dehydrogenase | / | 0.444 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.444 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.442 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.442 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.442 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.442 | |
| 1bdm | NAX | Malate dehydrogenase | / | 0.441 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.441 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.441 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.440 |