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 |
|---|---|---|---|
| 2qe0 | NAP | NADP-dependent glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.9 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2qe0 | NAP | NADP-dependent glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.9 | 1.000 | |
| 2euh | NAP | NADP-dependent glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.9 | 0.638 | |
| 2esd | NAP | NADP-dependent glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.9 | 0.604 | |
| 1qi1 | NAP | NADP-dependent glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.9 | 0.571 | |
| 3rhh | NAP | NADP-dependent glyceraldehyde-3-phosphate dehydrogenase | / | 0.548 | |
| 4nmk | NAP | Aldehyde dehydrogenase | / | 0.504 | |
| 4i3v | NAD | Aldehyde dehydrogenase (NAD+) | / | 0.483 | |
| 4zuk | NAD | Alpha-aminoadipic semialdehyde dehydrogenase | 1.2.1.31 | 0.477 | |
| 4h73 | NDP | Aldehyde dehydrogenase | / | 0.473 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.470 | |
| 2xdr | NDP | NAD/NADP-dependent betaine aldehyde dehydrogenase | / | 0.466 | |
| 1uxn | NAP | NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase | / | 0.465 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.464 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.464 | |
| 4i3w | NAD | Aldehyde dehydrogenase (NAD+) | / | 0.464 | |
| 2ilt | NN1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.463 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.463 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.462 | |
| 4jlk | 1NO | Deoxycytidine kinase | 2.7.1.74 | 0.462 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.461 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.461 | |
| 4zvy | NAD | Alpha-aminoadipic semialdehyde dehydrogenase | 1.2.1.31 | 0.461 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.459 | |
| 1gjr | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.458 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.458 | |
| 3pgq | GY3 | Acetyl-CoA carboxylase | / | 0.455 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.454 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.454 | |
| 4pxn | NAD | Aldehyde dehydrogenase family 7 member B4 | / | 0.454 | |
| 2hen | ADP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.453 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.452 | |
| 3zcw | 4A2 | Kinesin-like protein KIF11 | / | 0.452 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 4l8u | 9AZ | Serum albumin | / | 0.452 | |
| 1xu9 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.451 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.450 | |
| 2x3n | FAD | Probable FAD-dependent monooxygenase | / | 0.450 | |
| 3m8p | 65B | Gag-Pol polyprotein | 2.7.7.49 | 0.450 | |
| 4l9q | 9TP | Serum albumin | / | 0.450 | |
| 1osv | CHC | Bile acid receptor | / | 0.449 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.449 | |
| 1aiq | CB3 | Thymidylate synthase | / | 0.448 | |
| 3ntg | D72 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.448 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.448 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.448 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.448 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.447 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.447 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.447 | |
| 4iak | ADP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.446 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 2j0d | ERY | Cytochrome P450 3A4 | / | 0.445 | |
| 3d5q | T30 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.445 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.444 | |
| 2hnz | PC0 | Gag-Pol polyprotein | 2.7.7.49 | 0.443 | |
| 4a9m | P9M | Bromodomain-containing protein 2 | / | 0.443 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.443 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.443 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.443 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.443 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.442 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.442 | |
| 3pgh | FLP | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.442 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.442 | |
| 2w4q | CBW | Prostaglandin reductase 2 | 1.3.1.48 | 0.441 | |
| 3h0a | D30 | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.441 | |
| 3vso | EK1 | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.441 | |
| 3h6k | 33T | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 3nf7 | CIW | Gag-Pol polyprotein | / | 0.440 | |
| 3qaq | QAQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.440 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.440 | |
| 4k5y | 1Q5 | Corticotropin-releasing factor receptor 1 | / | 0.440 |