sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1nqo | NAD | Glyceraldehyde-3-phosphate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1nqo | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 1.000 | |
| 1nq5 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.681 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.629 | |
| 3cmc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.609 | |
| 3e5r | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.609 | |
| 4p8r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.607 | |
| 3lvf | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.605 | |
| 3l4s | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.599 | |
| 1qxs | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.594 | |
| 1gyp | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.591 | |
| 3ksd | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.587 | |
| 1nqa | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.585 | |
| 3hja | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.585 | |
| 3cif | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.584 | |
| 1gd1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.581 | |
| 1a7k | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.578 | |
| 3dbv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.565 | |
| 3cps | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.564 | |
| 2vyn | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.563 | |
| 4k9d | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.561 | |
| 3k2b | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.559 | |
| 1ml3 | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.554 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.553 | |
| 1cer | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.552 | |
| 2vyv | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.543 | |
| 3dmt | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.539 | |
| 4o59 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.537 | |
| 3b20 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.531 | |
| 2g82 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.528 | |
| 3zdf | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.524 | |
| 1znq | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.523 | |
| 2pkr | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.517 | |
| 3qv1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.498 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.487 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.481 | |
| 1u8f | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.472 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.469 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.468 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.464 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.463 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.460 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.459 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.455 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.454 | |
| 2f1k | NAP | Prephenate dehydrogenase | / | 0.453 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.453 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.452 | |
| 4ajp | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.452 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.452 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.452 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.451 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.450 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.450 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.450 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.449 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.448 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.446 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.445 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.445 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.445 | |
| 2fze | APR | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.444 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.443 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.443 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.442 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.442 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.441 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.441 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.441 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.440 |