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 |
|---|---|---|---|
| 1f5n | GNP | Guanylate-binding protein 1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1f5n | GNP | Guanylate-binding protein 1 | / | 1.000 | |
| 4idp | GNP | Atlastin-1 | 3.6.5 | 0.479 | |
| 2bc9 | GNP | Guanylate-binding protein 1 | / | 0.478 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.474 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.474 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.474 | |
| 3e8x | NAP | BH1520 protein | / | 0.474 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.471 | |
| 3q5d | GDP | Atlastin-1 | 3.6.5 | 0.471 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.469 | |
| 1dlj | UGA | UDP-glucose 6-dehydrogenase | / | 0.467 | |
| 2g76 | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.467 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.466 | |
| 1kfb | IGP | Tryptophan synthase alpha chain | / | 0.461 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.461 | |
| 2jlc | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.460 | |
| 1pnv | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.458 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.457 | |
| 3d8b | ADP | Fidgetin-like protein 1 | 3.6.4 | 0.457 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.457 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.457 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.456 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.456 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.456 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.456 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.455 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.455 | |
| 4y9q | C2E | Uncharacterized protein | / | 0.455 | |
| 4g6g | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.454 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.452 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.452 | |
| 3qof | GDP | Atlastin-1 | 3.6.5 | 0.452 | |
| 1gle | ADP | Glycerol kinase | / | 0.450 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.450 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.450 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.450 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.449 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.449 | |
| 4e5p | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.449 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.449 | |
| 5bqf | NAP | Probable hydroxyacid dehydrogenase protein | / | 0.449 | |
| 2d4v | NAD | Isocitrate dehydrogenase [NADP] | / | 0.448 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.447 | |
| 3pxv | FMN | Nitroreductase | / | 0.447 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.447 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.447 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.447 | |
| 1tka | N3T | Transketolase 1 | 2.2.1.1 | 0.446 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.446 | |
| 3lfz | ATP | Uncharacterized protein MJ1225 | / | 0.446 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.446 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.446 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.445 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.445 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.444 | |
| 2nni | MTK | Cytochrome P450 2C8 | / | 0.444 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.444 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.443 | |
| 4ddh | MS0 | Pantothenate synthetase | 6.3.2.1 | 0.443 | |
| 4idn | GNP | Atlastin-1 | 3.6.5 | 0.443 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.443 | |
| 1svw | GTP | Probable GTP-binding protein EngB | / | 0.442 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.442 | |
| 2j09 | FMN | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.442 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.442 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 1um0 | FMN | Chorismate synthase | / | 0.441 | |
| 2b53 | D23 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.441 | |
| 3u9e | COA | Lmo1369 protein | / | 0.441 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.441 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.441 | |
| 1gld | ADP | Glycerol kinase | / | 0.440 | |
| 1hku | NAD | C-terminal-binding protein 1 | 1.1.1 | 0.440 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.440 | |
| 2dbq | NAP | Glyoxylate reductase | 1.1.1.26 | 0.440 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.440 | |
| 3bts | NAD | Galactose/lactose metabolism regulatory protein GAL80 | / | 0.440 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.440 |