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 |
|---|---|---|---|
| 3gwd | FAD | Cyclohexanone monooxygenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3gwd | FAD | Cyclohexanone monooxygenase | / | 1.000 | |
| 1w4x | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.516 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.515 | |
| 3djg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.508 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.506 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.504 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.498 | |
| 2ylx | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.492 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.489 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.489 | |
| 3vuc | HHE | Renin | 3.4.23.15 | 0.487 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.486 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.484 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.484 | |
| 2npx | NAD | NADH peroxidase | 1.11.1.1 | 0.484 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.484 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.483 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.483 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.482 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.481 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.481 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.480 | |
| 3g72 | A6T | Renin | 3.4.23.15 | 0.480 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.479 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.478 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.478 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.478 | |
| 1grb | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.473 | |
| 2ylr | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.473 | |
| 4d04 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.473 | |
| 1egd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.472 | |
| 1ng3 | FAD | Glycine oxidase | 1.4.3.19 | 0.471 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.471 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.471 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.471 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.470 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.470 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 2c3c | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.468 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.468 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.467 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.467 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.467 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.467 | |
| 2rgo | FAD | Alpha-Glycerophosphate Oxidase | / | 0.466 | |
| 2ylw | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.466 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.466 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.465 | |
| 2yls | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.465 | |
| 3dk9 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.465 | |
| 3uov | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.465 | |
| 3utf | FDA | UDP-galactopyranose mutase | / | 0.465 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 1k4q | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.464 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.464 | |
| 3dk4 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.464 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.463 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.463 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.463 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.463 | |
| 4gkv | NAD | Alcohol dehydrogenase, propanol-preferring | 1.1.1.1 | 0.463 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.462 | |
| 4tlz | FAD | KtzI | / | 0.462 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 1wam | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.461 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.461 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.459 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.459 | |
| 2v6o | FAD | Thioredoxin glutathione reductase | / | 0.459 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.459 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.459 | |
| 4ap3 | FAD | Steroid monooxygenase | / | 0.459 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.458 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.458 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.457 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.457 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.457 | |
| 2r9z | FAD | Glutathione amide reductase | / | 0.457 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.457 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.457 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.457 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.457 | |
| 1xha | R68 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.456 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.456 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 3pfd | FDA | Acyl-CoA dehydrogenase FadE25 | / | 0.455 | |
| 4tm4 | FDA | KtzI | / | 0.455 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.455 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.454 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.454 | |
| 3oag | LPQ | Renin | 3.4.23.15 | 0.454 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.454 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.454 | |
| 4tlx | FDA | KtzI | / | 0.454 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.454 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.453 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.453 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2bac | FAD | Putative aminooxidase | / | 0.453 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.453 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.453 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.453 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.453 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.453 | |
| 4gid | 0GH | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.452 | |
| 1tj1 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.452 | |
| 3own | 3OX | Renin | 3.4.23.15 | 0.452 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 4nwz | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.452 | |
| 4u8i | FDA | UDP-galactopyranose mutase | / | 0.452 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.452 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.451 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.451 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.451 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.451 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.451 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.451 | |
| 1grh | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.450 | |
| 2bi8 | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.450 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.450 | |
| 4iv6 | FDA | Isovaleryl-CoA dehydrogenase | / | 0.450 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.449 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.449 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.449 | |
| 1gre | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.448 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.448 | |
| 3bgb | LJG | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.448 | |
| 3owa | FAD | Acyl-CoA dehydrogenase | / | 0.448 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.447 | |
| 1gra | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.447 | |
| 1grg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.447 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.447 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.447 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.447 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.447 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.447 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4c3y | FAD | 3-ketosteroid dehydrogenase | / | 0.447 | |
| 4irn | FAD | AnaB | / | 0.447 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.447 | |
| 4u8k | FDA | UDP-galactopyranose mutase | / | 0.447 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.446 | |
| 2ym2 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.446 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.446 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.446 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.446 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.446 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.446 | |
| 4isk | 1JY | Thymidylate synthase | / | 0.446 | |
| 1iy8 | NAD | Levodione reductase | / | 0.445 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.445 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.445 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.445 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1get | FAD | Glutathione reductase | 1.8.1.7 | 0.444 | |
| 1hdo | NAP | Flavin reductase (NADPH) | / | 0.444 | |
| 1kqf | MGD | Formate dehydrogenase, nitrate-inducible, major subunit | 1.1.5.6 | 0.444 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.444 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.444 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.444 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.444 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.444 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.444 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.444 | |
| 1gqt | ACP | Ribokinase | / | 0.443 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 1ve9 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.443 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.443 | |
| 2fsv | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.443 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.443 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3sqp | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.443 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.443 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.443 | |
| 4aos | FAD | Steroid monooxygenase | / | 0.443 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.443 | |
| 2bi7 | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.442 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.442 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.442 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2cfy | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.441 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.441 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.441 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.441 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 2ylt | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.441 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.441 | |
| 3t88 | S0N | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.441 | |
| 4c4o | NAD | SADH | / | 0.441 | |
| 4p63 | NAD | Probable deoxyhypusine synthase | 2.5.1.46 | 0.441 | |
| 4tm3 | FAD | KtzI | / | 0.441 | |
| 5dcy | NAP | Iridoid synthase | 1.3.1.99 | 0.441 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.440 | |
| 1hld | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.440 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.440 | |
| 2g27 | 4LG | Renin | 3.4.23.15 | 0.440 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.440 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.440 | |
| 2pob | GW4 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2xgs | 44P | Uncharacterized protein | / | 0.440 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.440 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.440 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.440 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.440 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 5hsa | FAS | Alcohol oxidase 1 | 1.1.3.13 | 0.440 |