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 |
|---|---|---|---|
| 1zdf | UPG | Glycogenin-1 | 2.4.1.186 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1zdf | UPG | Glycogenin-1 | 2.4.1.186 | 1.000 | |
| 1zdg | UPG | Glycogenin-1 | 2.4.1.186 | 0.609 | |
| 3rmw | UPG | Glycogenin-1 | 2.4.1.186 | 0.542 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.513 | |
| 2e1z | B4P | Propionate kinase | / | 0.501 | |
| 5c3a | URM | Histo-blood group ABO system transferase | / | 0.494 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.493 | |
| 1g93 | UPG | N-acetyllactosaminide alpha-1,3-galactosyltransferase | / | 0.487 | |
| 5c1l | GDU | Histo-blood group ABO system transferase | / | 0.470 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.466 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.464 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.463 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.462 | |
| 5c3b | URM | Histo-blood group ABO system transferase | / | 0.462 | |
| 1nmd | ATP | Major actin | / | 0.461 | |
| 3img | BZ3 | Pantothenate synthetase | 6.3.2.1 | 0.461 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.460 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.460 | |
| 4e5h | 0N8 | Polymerase acidic protein | / | 0.460 | |
| 5c48 | URM | Histo-blood group ABO system transferase | / | 0.459 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.458 | |
| 1dfo | PLG | Serine hydroxymethyltransferase | 2.1.2.1 | 0.456 | |
| 1g9b | BAB | Botulinum neurotoxin type B | 3.4.24.69 | 0.456 | |
| 1rfq | LAR | Actin, alpha skeletal muscle | / | 0.456 | |
| 2j0s | ANP | Eukaryotic initiation factor 4A-III | 3.6.4.13 | 0.455 | |
| 3pft | FMN | Flavin reductase | / | 0.455 | |
| 4yqf | GDP | Septin-9 | / | 0.455 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.454 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.453 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.453 | |
| 1eqb | FFO | Serine hydroxymethyltransferase | 2.1.2.1 | 0.451 | |
| 3gon | ANP | Phosphomevalonate kinase | / | 0.451 | |
| 3t7v | SAM | 3-methylornithine synthase | / | 0.451 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.451 | |
| 3gnq | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.450 | |
| 3qcx | 3Q2 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.450 | |
| 2e20 | B4P | Propionate kinase | / | 0.449 | |
| 4ddh | MS0 | Pantothenate synthetase | 6.3.2.1 | 0.449 | |
| 1tou | B1V | Fatty acid-binding protein, adipocyte | / | 0.448 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.448 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.448 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.447 | |
| 3l3l | L3L | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.447 | |
| 4ts7 | ADP | Purine phosphoribosyltransferase (GpT-1) | / | 0.447 | |
| 2db3 | ANP | ATP-dependent RNA helicase vasa, isoform A | 3.6.4.13 | 0.446 | |
| 3jsz | UPG | Uncharacterized protein | / | 0.446 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.445 | |
| 2cdu | FAD | NADH oxidase | / | 0.445 | |
| 2vkd | UPG | Cytotoxin L | / | 0.445 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.445 | |
| 4req | 5AD | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.445 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.444 | |
| 3af3 | GCP | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.444 | |
| 1gox | FMN | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.443 | |
| 1qwj | NCC | N-acylneuraminate cytidylyltransferase | 2.7.7.43 | 0.443 | |
| 2j5b | TYE | Tyrosine--tRNA ligase | 6.1.1.1 | 0.443 | |
| 3i5x | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.443 | |
| 4e5l | DBH | Polymerase acidic protein | / | 0.443 | |
| 1zp4 | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.442 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.442 | |
| 5c3j | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.442 | |
| 1g9a | BAB | Botulinum neurotoxin type B | 3.4.24.69 | 0.441 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 3t7q | RB4 | Endothiapepsin | 3.4.23.22 | 0.441 | |
| 1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.440 | |
| 3iob | A4D | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 5c2t | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.440 |