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 |
|---|---|---|---|
| 2adm | SAM | Modification methylase TaqI | 2.1.1.72 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2adm | SAM | Modification methylase TaqI | 2.1.1.72 | 1.000 | |
| 2ih5 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.540 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.487 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.484 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.474 | |
| 2np6 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.473 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.468 | |
| 3dxm | N24 | Actin-related protein 3 | / | 0.466 | |
| 1iy8 | NAD | Levodione reductase | / | 0.464 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.464 | |
| 1d7a | AIR | N5-carboxyaminoimidazole ribonucleotide mutase | / | 0.462 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.462 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.461 | |
| 4m10 | ICD | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.459 | |
| 3q71 | AR6 | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.458 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.458 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.457 | |
| 5dp2 | NAP | CurF | / | 0.456 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.455 | |
| 5c2t | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.454 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.453 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.453 | |
| 3bgc | LJH | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.453 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.452 | |
| 1udb | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.452 | |
| 3q33 | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.452 | |
| 4m11 | MXM | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.452 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.451 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.451 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.450 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.450 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.450 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.449 | |
| 2idw | 017 | Protease | / | 0.449 | |
| 1qf4 | RPD | Adenylosuccinate synthetase | / | 0.448 | |
| 1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 2e4n | SAH | Diphthine synthase | / | 0.448 | |
| 3nn6 | FB0 | 6-hydroxy-L-nicotine oxidase | / | 0.448 | |
| 4kz0 | 1UJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 4uir | FAD | Oleate hydratase | 4.2.1.53 | 0.448 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.448 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.447 | |
| 2pwc | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.447 | |
| 3m13 | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.447 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.447 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.447 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.446 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.446 | |
| 3if9 | FAD | Glycine oxidase | 1.4.3.19 | 0.446 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.446 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.446 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.446 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.445 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.445 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.445 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.445 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.445 | |
| 4n82 | FMN | Ribonucleotide reductase (NrdI family protein), putative | / | 0.445 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.445 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4gev | CB3 | Thymidylate synthase | / | 0.444 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.444 | |
| 4ke0 | 1R8 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4l4x | NDP | AmphI | / | 0.444 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.444 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.444 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1rbz | KT5 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.443 | |
| 2ejz | SAH | Diphthine synthase | / | 0.443 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.443 | |
| 2oa7 | GTX | Glutathione S-transferase P 1 | 2.5.1.18 | 0.443 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.443 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.443 | |
| 3q8h | AO9 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.443 | |
| 4h1v | GNP | Dynamin-1-like protein | 3.6.5.5 | 0.443 | |
| 5c93 | ACP | Two-component system histidine protein kinase | / | 0.443 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1cjw | COT | Serotonin N-acetyltransferase | / | 0.442 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.442 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.442 | |
| 2pch | SAH | Diphthine synthase | / | 0.442 | |
| 3qrs | NK8 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.442 | |
| 3zbz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 4e9a | QAP | Peptide deformylase | / | 0.442 | |
| 4eu5 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.442 | |
| 4i6a | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.442 | |
| 4ih7 | 1ER | Genome polyprotein | 2.7.7.48 | 0.442 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2dsh | SAH | Diphthine synthase | / | 0.441 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.441 | |
| 2wkz | 5AH | Gag-Pol polyprotein | / | 0.441 | |
| 2xb5 | I7T | Tetracycline repressor protein class D | / | 0.441 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.441 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.441 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.441 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.441 | |
| 1c2t | NHS | Phosphoribosylglycinamide formyltransferase | / | 0.440 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.440 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.440 | |
| 1zsk | 421 | Coagulation factor XI | 3.4.21.27 | 0.440 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.440 | |
| 2dsg | SAH | Diphthine synthase | / | 0.440 | |
| 2gv8 | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.440 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.440 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.440 | |
| 3l9h | EMQ | Kinesin-like protein KIF11 | / | 0.440 |