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 |
|---|---|---|---|
| 4eqk | MGT | Polymerase basic protein 2 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4eqk | MGT | Polymerase basic protein 2 | / | 1.000 | |
| 4nce | MGT | Polymerase basic protein 2 | / | 0.579 | |
| 4cb6 | 29R | Polymerase basic protein 2 | / | 0.563 | |
| 2vqz | MGT | Polymerase basic protein 2 | / | 0.549 | |
| 5fmm | MGT | Polymerase basic protein 2 | / | 0.543 | |
| 4cb5 | 93G | Polymerase basic protein 2 | / | 0.490 | |
| 2cda | NAP | Glucose 1-dehydrogenase | / | 0.489 | |
| 4cb7 | 41G | Polymerase basic protein 2 | / | 0.489 | |
| 4cb4 | MGT | Polymerase basic protein 2 | / | 0.487 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.478 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.478 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.477 | |
| 4es5 | MGT | Polymerase basic protein 2 | / | 0.476 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 4dz5 | NAP | Aldo-keto reductase family 1 member C3 | / | 0.464 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.462 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.461 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.461 | |
| 3zj7 | C1K | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.461 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.461 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 2qcx | PF1 | Aminopyrimidine aminohydrolase | / | 0.457 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.456 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.455 | |
| 2qf2 | GDP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.455 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.454 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3c1o | NAP | Eugenol synthase | / | 0.453 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 1q20 | PLO | Sulfotransferase family cytosolic 2B member 1 | 2.8.2.2 | 0.451 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.451 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.451 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.450 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.450 | |
| 3ha3 | SAH | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.450 | |
| 1s1r | NAP | Aldo-keto reductase family 1 member C3 | / | 0.449 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.449 | |
| 3gf4 | U5P | UDP-galactopyranose mutase | 5.4.99.9 | 0.449 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.447 | |
| 2zyn | BCD | Periplasmic binding protein | / | 0.447 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.447 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.447 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3s8p | SAM | Histone-lysine N-methyltransferase KMT5B | 2.1.1.43 | 0.446 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.446 | |
| 4e2b | FMN | Dehydrogenase | / | 0.446 | |
| 1cjt | FOK | Adenylate cyclase type 2 | / | 0.445 | |
| 1cjt | FOK | Adenylate cyclase type 5 | / | 0.445 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 4e2d | FMN | Dehydrogenase | / | 0.445 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.445 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 3cop | ADP | Glycogen synthase | 2.4.1.21 | 0.444 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2z4w | 749 | Geranylgeranyl pyrophosphate synthase | / | 0.443 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.442 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.442 | |
| 4e0u | 0MV | Cyclic dipeptide N-prenyltransferase | / | 0.442 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 2ft0 | ACO | dTDP-fucosamine acetyltransferase | / | 0.441 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.441 | |
| 2xlp | NAP | Putative flavin-containing monooxygenase | / | 0.441 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.441 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.441 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 4isg | 1FY | Glucokinase | 2.7.1.2 | 0.441 | |
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.441 | |
| 4wx2 | F6F | Tryptophan synthase alpha chain | / | 0.441 | |
| 4wx2 | F6F | Tryptophan synthase beta chain | 4.2.1.20 | 0.441 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.440 |