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 |
|---|---|---|---|
| 2iib | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2iib | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 1.000 | |
| 2ex1 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.649 | |
| 2ilv | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.635 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.471 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.471 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.469 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.469 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.468 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.466 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.464 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.463 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.462 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.461 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.461 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.461 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.460 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.460 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.458 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.458 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.458 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.457 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.457 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.457 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.454 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.454 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.454 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.453 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.452 | |
| 1r6t | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.451 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.451 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.451 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.451 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.451 | |
| 3n14 | FMN | Xenobiotic reductase | / | 0.451 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.450 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.450 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 3kxw | 1ZZ | Saframycin Mx1 synthetase B | / | 0.449 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.449 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.448 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.448 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.447 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.447 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.447 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.446 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.446 | |
| 2yd0 | BES | Endoplasmic reticulum aminopeptidase 1 | 3.4.11 | 0.446 | |
| 3gnv | XNZ | Genome polyprotein | 2.7.7.48 | 0.446 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.445 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.444 | |
| 4usr | FAD | Monooxygenase | / | 0.444 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.443 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.443 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.443 | |
| 3oet | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.443 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.443 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.443 | |
| 4c5o | FAD | Putative monooxygenase | / | 0.443 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.443 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.443 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.442 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.442 | |
| 3kpb | SAM | Uncharacterized protein MJ0100 | / | 0.442 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.442 | |
| 3pft | FMN | Flavin reductase | / | 0.442 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.442 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 2dgn | DOI | Adenylosuccinate synthetase isozyme 1 | / | 0.441 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.441 | |
| 3lqs | PSZ | D-alanine aminotransferase | 2.6.1.21 | 0.441 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.440 | |
| 4usq | FAD | Pyridine nucleotide-disulfide oxidoreductase | / | 0.440 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.440 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.440 |