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 |
|---|---|---|---|
| 4col | DTP | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4col | DTP | Uncharacterized protein | / | 1.000 | |
| 3mx5 | UTP | Nucleoprotein | / | 0.483 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.479 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.478 | |
| 2vrx | 447 | Aurora kinase B-A | 2.7.11.1 | 0.471 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.466 | |
| 4o9k | CMK | Arabinose 5-phosphate isomerase | / | 0.466 | |
| 4u0z | APC | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.466 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.460 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.460 | |
| 4coj | DTP | Uncharacterized protein | / | 0.457 | |
| 1n2j | PAF | Pantothenate synthetase | 6.3.2.1 | 0.456 | |
| 2w7x | D1A | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.456 | |
| 3anm | SYD | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.455 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.455 | |
| 4xf7 | ACP | Carbohydrate/pyrimidine kinase, PfkB family | / | 0.455 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.454 | |
| 2nua | COA | Succinate--CoA ligase [ADP-forming] subunit alpha | 6.2.1.5 | 0.453 | |
| 4im0 | 1FV | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.452 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.451 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.451 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 1w48 | APC | NTPase P4 | / | 0.450 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.450 | |
| 4tvb | NAD | Homospermidine synthase | 2.5.1.44 | 0.450 | |
| 1r6t | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.449 | |
| 1n77 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.448 | |
| 4a0r | DTB | Bifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial | 6.3.3.3 | 0.448 | |
| 4uz6 | SCR | Palmitoleoyl-protein carboxylesterase NOTUM | / | 0.448 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.448 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.447 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.446 | |
| 3uk6 | ADP | RuvB-like 2 | 3.6.4.12 | 0.446 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.445 | |
| 3ieu | GDP | GTPase Era | / | 0.445 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.444 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.444 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.444 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.443 | |
| 2e94 | 364 | Geranylgeranyl pyrophosphate synthase | / | 0.443 | |
| 1iy8 | NAD | Levodione reductase | / | 0.442 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.442 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.442 | |
| 2w0j | ZAT | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.442 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3lxd | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.442 | |
| 3w6u | NAP | 6-phosphogluconate dehydrogenase, NAD-binding protein | / | 0.442 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.441 | |
| 3bt9 | DEQ | HTH-type transcriptional regulator QacR | / | 0.441 | |
| 3mx2 | TTP | Nucleoprotein | / | 0.441 | |
| 3bbr | BHY | Glutamate receptor 2 | / | 0.440 | |
| 3coz | 54H | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 3ivx | FG6 | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 |