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 |
|---|---|---|---|
| 1xd9 | ADP | Nitrogenase iron protein 1 | 1.18.6.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1xd9 | ADP | Nitrogenase iron protein 1 | 1.18.6.1 | 1.000 | |
| 4axd | ANP | Inositol-pentakisphosphate 2-kinase | 2.7.1.158 | 0.476 | |
| 2xsz | ATP | RuvB-like 2 | 3.6.4.12 | 0.468 | |
| 3ge1 | ADP | Glycerol kinase | / | 0.464 | |
| 2cmv | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.461 | |
| 2o12 | FMN | Chorismate synthase | / | 0.461 | |
| 3t54 | ATP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.460 | |
| 2y4g | TIR | TamL | / | 0.459 | |
| 4b3a | TAC | Tetracycline repressor protein class D | / | 0.459 | |
| 3a1e | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.458 | |
| 3oqu | A8S | Abscisic acid receptor PYL9 | / | 0.458 | |
| 2dpx | GDP | GTP-binding protein RAD | / | 0.457 | |
| 2xb5 | I7T | Tetracycline repressor protein class D | / | 0.457 | |
| 1gsf | EAA | Glutathione S-transferase A1 | 2.5.1.18 | 0.456 | |
| 3cvu | FAD | RE11660p | / | 0.456 | |
| 2dfd | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.455 | |
| 4d7m | TDC | Tetracycline repressor protein class D | / | 0.455 | |
| 5fkm | TDC | Tetracycline repressor protein class D | / | 0.454 | |
| 3ea0 | ATP | ATPase, ParA family | / | 0.453 | |
| 3uvq | FS8 | Mitogen-activated protein kinase 14 | / | 0.453 | |
| 4z69 | DIF | Serum albumin | / | 0.453 | |
| 1q3s | ADP | Thermosome subunit alpha | / | 0.452 | |
| 5fkn | TDC | Tetracycline repressor protein class D | / | 0.452 | |
| 3qai | XNN | Ketohexokinase | / | 0.451 | |
| 4o6m | C5P | Uncharacterized protein | / | 0.450 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 2x0q | ATP | Alcaligin biosynthesis protein | / | 0.449 | |
| 2o7o | DXT | Tetracycline repressor protein class D | / | 0.448 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.448 | |
| 1omo | NAD | Alanine dehydrogenase | / | 0.447 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.445 | |
| 4axf | ANP | Inositol-pentakisphosphate 2-kinase | 2.7.1.158 | 0.444 | |
| 4h50 | NAP | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.444 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.443 | |
| 2xpv | MIY | Tetracycline repressor protein class D | / | 0.442 | |
| 3uwq | U5P | Orotidine 5'-phosphate decarboxylase | / | 0.442 | |
| 1nlm | UD1 | UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase | / | 0.441 | |
| 4h0y | LAR | Actin, alpha skeletal muscle | / | 0.441 | |
| 4l04 | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.441 | |
| 2jds | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2ohx | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 | |
| 3cf0 | ADP | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.440 | |
| 4pd6 | URI | Nucleoside permease | / | 0.440 |