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 |
|---|---|---|---|
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 1.000 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.628 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.592 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.496 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.494 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.480 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.478 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.474 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.472 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.471 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.471 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.470 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.468 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.466 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.466 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.466 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.465 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.465 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.465 | |
| 1cnf | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.464 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.464 | |
| 3int | GDU | UDP-galactopyranose mutase | 5.4.99.9 | 0.464 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.464 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.462 | |
| 1daa | PLP | D-alanine aminotransferase | 2.6.1.21 | 0.461 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.460 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.460 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.460 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.459 | |
| 1x27 | ASP_TYR_VAL_HIS_PTR | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.459 | |
| 2bt4 | CA2 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.459 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.458 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.458 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.458 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.457 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 1e0j | ANP | DNA primase/helicase | 2.7.7 | 0.456 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.456 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.456 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.456 | |
| 3qiz | QI2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.456 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.456 | |
| 3rba | COD | Phosphopantetheine adenylyltransferase | / | 0.455 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.454 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.453 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.453 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.453 | |
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 0.453 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.452 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.452 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.452 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.452 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.452 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.452 | |
| 1kh3 | ANP | Argininosuccinate synthase | / | 0.451 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.450 | |
| 2f98 | NGV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.450 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.450 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.450 | |
| 4fdn | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.450 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2zsh | GA3 | Gibberellin receptor GID1A | 3 | 0.449 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.449 | |
| 4jey | PLP | Acetylornithine/succinyldiaminopimelate aminotransferase | 2.6.1.11 | 0.449 | |
| 2ejz | SAH | Diphthine synthase | / | 0.448 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.448 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.448 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.448 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.447 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.447 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.447 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 1n2h | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.446 | |
| 1s4o | GDP | Glycolipid 2-alpha-mannosyltransferase | / | 0.446 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.446 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.446 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.446 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.446 | |
| 4rnu | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.446 | |
| 5c1d | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.446 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.445 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.445 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.445 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.445 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 1npd | NAD | Quinate/shikimate dehydrogenase | / | 0.444 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.444 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.444 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.443 | |
| 1udb | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.443 | |
| 1ytm | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.443 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.443 | |
| 3hl4 | CDC | Choline-phosphate cytidylyltransferase A | / | 0.443 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.443 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.443 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.442 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 2e1m | FAD | L-glutamate oxidase | / | 0.442 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.442 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.442 | |
| 2e0a | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.441 | |
| 2vat | COA | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.441 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.441 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.441 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.440 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.440 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.440 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.440 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.440 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.440 | |
| 4e2d | FMN | Dehydrogenase | / | 0.440 |