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 |
|---|---|---|---|
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 1.000 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.605 | |
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 0.550 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.495 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.484 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.482 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.480 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.475 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.472 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.472 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.471 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.470 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.469 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.468 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.466 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.466 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.465 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.465 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.464 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.464 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.462 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.461 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.460 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.457 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.457 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.455 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.455 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.454 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.454 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.454 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.454 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.453 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.453 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.452 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.452 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.451 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.451 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.450 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.450 | |
| 2aba | STR | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 2anb | 5GP | Guanylate kinase | 2.7.4.8 | 0.449 | |
| 2z3n | PHE_ARG_TYR_LEU_GLY | Leucyl/phenylalanyl-tRNA--protein transferase | 2.3.2.6 | 0.449 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.449 | |
| 4ike | ADP | Adenylate kinase | / | 0.449 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.448 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.448 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.447 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.446 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.446 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.445 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.444 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.444 | |
| 3r96 | ACO | MccE protein | / | 0.444 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.444 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.444 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.443 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.442 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.442 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.442 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.441 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.441 | |
| 1zp4 | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.441 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3axk | NDP | Ribulose bisphosphate carboxylase large chain | 4.1.1.39 | 0.441 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.441 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.441 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.440 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.440 | |
| 2ilv | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.440 | |
| 2ql6 | ADP | Nicotinamide riboside kinase 1 | / | 0.440 | |
| 4bqz | GNP | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.440 |