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 |
|---|---|---|---|
| 4rvn | COA | Phenylacetate-coenzyme A ligase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 1.000 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.478 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.477 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.475 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.474 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.472 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.468 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.466 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.465 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.464 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.462 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.461 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.461 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.460 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.459 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.459 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.459 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.459 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.458 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.457 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.455 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.455 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.454 | |
| 2ylw | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.454 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.454 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.454 | |
| 2ylr | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.453 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.452 | |
| 2vqb | FAD | Putative flavin-containing monooxygenase | / | 0.452 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.452 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.451 | |
| 2xvh | FAD | Putative flavin-containing monooxygenase | / | 0.450 | |
| 3iaa | TYD | CalG2 | / | 0.450 | |
| 3spt | UD1 | Bifunctional protein GlmU | / | 0.449 | |
| 1mzs | 669 | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | / | 0.448 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.448 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.448 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.448 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.448 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 1p0h | COA | Mycothiol acetyltransferase | 2.3.1.189 | 0.447 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.447 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.447 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.446 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4o67 | 1SY | Cyclic GMP-AMP synthase | / | 0.446 | |
| 2g2z | COZ | Malonyl CoA-acyl carrier protein transacylase | 2.3.1.39 | 0.445 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.445 | |
| 1ozp | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.444 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.444 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.444 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.444 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1jkx | 138 | Phosphoribosylglycinamide formyltransferase | / | 0.443 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.443 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.443 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.443 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.443 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.443 | |
| 1gqt | ACP | Ribokinase | / | 0.442 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.442 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.442 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 3ii4 | 3II | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.442 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.442 | |
| 1o0s | NAI | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.441 | |
| 1p3d | UMA | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.441 | |
| 2p2m | PRX | Acetyl-coenzyme A synthetase | / | 0.441 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.441 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.441 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.441 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.440 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.440 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.440 | |
| 2ylt | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.440 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.440 | |
| 3biy | 01K | Histone acetyltransferase p300 | / | 0.440 | |
| 5c77 | SAH | Protein arginine N-methyltransferase SFM1 | / | 0.440 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.440 |