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 |
|---|---|---|---|
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 1.000 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.497 | |
| 4pao | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.493 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.481 | |
| 2rl1 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.476 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.476 | |
| 3c14 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.475 | |
| 3cx8 | GSP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.472 | |
| 3c15 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.469 | |
| 2qtv | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.468 | |
| 3vgl | ANP | Glucokinase | / | 0.468 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.466 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.464 | |
| 2olq | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.463 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.463 | |
| 1dj3 | GDP | Adenylosuccinate synthetase, chloroplastic | / | 0.462 | |
| 3upk | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.462 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.462 | |
| 2olr | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.461 | |
| 5cwa | 0GA | Anthranilate synthase component 1 | 4.1.3.27 | 0.461 | |
| 1yon | A2R | 2-dehydropantoate 2-reductase | 1.1.1.169 | 0.460 | |
| 2g78 | REA | Cellular retinoic acid-binding protein 2 | / | 0.460 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.460 | |
| 2yvw | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.459 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.458 | |
| 1gil | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.457 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.455 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.455 | |
| 3cx6 | GDP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.455 | |
| 1esv | LAR | Actin, alpha skeletal muscle | / | 0.454 | |
| 5k5z | ANP | Uncharacterized protein | / | 0.454 | |
| 2oor | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.453 | |
| 3lov | FAD | Protoporphyrinogen oxidase | / | 0.453 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.453 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.452 | |
| 2ya3 | J7V | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.450 | |
| 3r9x | GNP | GTPase Era | / | 0.450 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.448 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.448 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.448 | |
| 3qw4 | U5P | Orotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative | / | 0.447 | |
| 3swq | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.446 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.446 | |
| 1het | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 3c16 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.445 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.445 | |
| 3mx5 | UTP | Nucleoprotein | / | 0.445 | |
| 4a6c | QG9 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 4d0l | GSP | Ras-related protein Rab-11A | / | 0.445 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.445 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.445 | |
| 1azt | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.444 | |
| 1t7j | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.444 | |
| 3cis | ATP | Universal stress protein Rv2623 | / | 0.444 | |
| 3tz3 | B36 | Acetyl-CoA carboxylase | / | 0.444 | |
| 4nxu | ADP | Mitochondrial dynamics protein MID51 | / | 0.444 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 2zvc | SAH | Precorrin-3 C17-methyltransferase | / | 0.443 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.443 | |
| 4xd2 | NAI | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.443 | |
| 3h86 | AP5 | Adenylate kinase | / | 0.442 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.442 | |
| 1qpj | STU | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.441 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.441 | |
| 3iss | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.441 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.441 | |
| 2eud | GCQ | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.440 | |
| 4i02 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.440 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.440 | |
| 5aga | ANP | DNA polymerase theta | / | 0.440 | |
| 5kj6 | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 |