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 |
|---|---|---|---|
| 5gpb | GPM | Glycogen phosphorylase, muscle form | 2.4.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5gpb | GPM | Glycogen phosphorylase, muscle form | 2.4.1.1 | 1.000 | |
| 4gpb | GFP | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.727 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.484 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.472 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.460 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.459 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.455 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.455 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.454 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.454 | |
| 1kqn | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.453 | |
| 4emw | FAD | Coenzyme A disulfide reductase | / | 0.453 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.452 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.452 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.452 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.452 | |
| 4el5 | D1M | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.452 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.450 | |
| 1nhp | FAD | NADH peroxidase | 1.11.1.1 | 0.449 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4i6a | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.449 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.448 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.448 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.447 | |
| 3dgh | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.447 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.446 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 1eq2 | ADQ | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.445 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.445 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.445 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 1o0s | NAI | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.443 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.443 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.443 | |
| 3enk | UPG | UDP-glucose 4-epimerase | / | 0.443 | |
| 3a5y | KAA | Elongation factor P--(R)-beta-lysine ligase | / | 0.442 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.442 | |
| 3t4n | ADP | 5'-AMP-activated protein kinase subunit gamma | / | 0.442 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.442 | |
| 3a3g | DLZ | Lumazine protein | / | 0.441 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.441 | |
| 1hku | NAD | C-terminal-binding protein 1 | 1.1.1 | 0.440 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.440 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.440 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.440 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.440 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.440 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.440 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.440 |