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 |
|---|---|---|---|
| 4ozt | P1A | Ecdysone receptor, putative |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4ozt | P1A | Ecdysone receptor, putative | / | 1.000 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.493 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.492 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.479 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.476 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.476 | |
| 5dp2 | NAP | CurF | / | 0.476 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.474 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.473 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.471 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.471 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.469 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.466 | |
| 3p4t | FAO | Putative acyl-CoA dehydrogenase | / | 0.466 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.466 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.465 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.465 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.464 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.464 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.464 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.463 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.463 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.463 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.462 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.462 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.462 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.461 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.460 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.459 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.459 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3eku | CY9 | Actin-5C | / | 0.459 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.459 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.458 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.458 | |
| 3ieu | GDP | GTPase Era | / | 0.458 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.457 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.457 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.457 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.457 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.457 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.456 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.456 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.456 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.456 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.455 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.454 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.453 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.453 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.453 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.453 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.452 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.452 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.452 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.452 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.452 | |
| 4e4q | RRH | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.451 | |
| 3a3g | DLZ | Lumazine protein | / | 0.451 | |
| 3fcj | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.451 | |
| 4b7x | NAP | Probable oxidoreductase | / | 0.451 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.451 | |
| 4qe6 | JN3 | Bile acid receptor | / | 0.451 | |
| 1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.450 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.449 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.449 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.448 | |
| 2bfq | AR6 | [Protein ADP-ribosylglutamate] hydrolase AF_1521 | 3.2.2 | 0.448 | |
| 3cvu | FAD | RE11660p | / | 0.448 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.448 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.447 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.447 | |
| 3eks | CY9 | Actin-5C | / | 0.447 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.447 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.447 | |
| 1opm | IYG | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.446 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.446 | |
| 2c0c | NAP | Prostaglandin reductase 3 | 1 | 0.446 | |
| 2uuv | FAD | Alkyldihydroxyacetonephosphate synthase | 2.5.1.26 | 0.446 | |
| 3owa | FAD | Acyl-CoA dehydrogenase | / | 0.446 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.446 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.446 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.446 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.446 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.446 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.445 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 3a3y | OBN | Sodium/potassium-transporting ATPase subunit alpha | / | 0.445 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.445 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.444 | |
| 1sdw | IYT | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.444 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.444 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.444 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.444 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.443 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.443 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.443 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.443 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.443 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.443 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.442 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.442 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.442 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.442 | |
| 1p0f | NAP | NADP-dependent alcohol dehydrogenase | 1.1.1.2 | 0.441 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.441 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.441 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.441 | |
| 4nwz | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.441 | |
| 1xu7 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.440 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.440 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.440 | |
| 4c0b | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.440 | |
| 4irn | FAD | AnaB | / | 0.440 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.440 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.440 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.440 |