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 |
|---|---|---|---|
| 3gwd | FAD | Cyclohexanone monooxygenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3gwd | FAD | Cyclohexanone monooxygenase | / | 1.000 | |
| 1w4x | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.505 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.504 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.502 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.500 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.497 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.492 | |
| 3djg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.490 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.484 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.482 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.482 | |
| 2ylx | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.481 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.478 | |
| 2npx | NAD | NADH peroxidase | 1.11.1.1 | 0.475 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.475 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.475 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.474 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.474 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.474 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.473 | |
| 3vuc | HHE | Renin | 3.4.23.15 | 0.473 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.473 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.471 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.469 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.469 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.468 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.468 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.467 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.466 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.466 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.466 | |
| 3g72 | A6T | Renin | 3.4.23.15 | 0.465 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.463 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.461 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.461 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.461 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.461 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.460 | |
| 1grb | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.458 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.458 | |
| 2c3c | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.458 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.458 | |
| 3dl0 | AP5 | Adenylate kinase | / | 0.458 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.457 | |
| 3dk4 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.457 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.457 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.457 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.457 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.456 | |
| 2yls | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.456 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.455 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.455 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.455 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.454 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.454 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.454 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.453 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.453 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.453 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.453 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.453 | |
| 4d04 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.453 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.452 | |
| 1xha | R68 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.451 | |
| 2vce | U2F | UDP-glycosyltransferase 72B1 | / | 0.451 | |
| 4bqu | CLR | Japanin | / | 0.451 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.450 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.450 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.450 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.449 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3dk9 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.449 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.449 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.449 | |
| 4gkv | NAD | Alcohol dehydrogenase, propanol-preferring | 1.1.1.1 | 0.449 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.449 | |
| 1ksz | PGS | Adenylosuccinate synthetase | / | 0.448 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.448 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.448 | |
| 3l9h | EMQ | Kinesin-like protein KIF11 | / | 0.448 | |
| 3ut5 | LOC | Tubulin beta chain | / | 0.448 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.448 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.448 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.447 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.447 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.447 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.447 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.447 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.447 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.446 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.446 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3own | 3OX | Renin | 3.4.23.15 | 0.446 | |
| 4tlz | FAD | KtzI | / | 0.446 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.445 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.445 | |
| 2bac | FAD | Putative aminooxidase | / | 0.445 | |
| 2g27 | 4LG | Renin | 3.4.23.15 | 0.445 | |
| 3oag | LPQ | Renin | 3.4.23.15 | 0.445 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.445 | |
| 4gid | 0GH | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4tlx | FDA | KtzI | / | 0.445 | |
| 4zwm | PLP | Ornithine aminotransferase, mitochondrial, putative | / | 0.445 | |
| 1egd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.444 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.444 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.444 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.444 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.444 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.444 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.444 | |
| 2ylw | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.444 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.443 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1gqt | ACP | Ribokinase | / | 0.443 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.443 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.443 | |
| 2irz | I02 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2r9z | FAD | Glutathione amide reductase | / | 0.443 | |
| 2ydb | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.443 | |
| 2ylr | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.443 | |
| 3bgb | LJG | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.443 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.443 | |
| 3pfd | FDA | Acyl-CoA dehydrogenase FadE25 | / | 0.443 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1llu | NAD | Alcohol dehydrogenase | / | 0.442 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.442 | |
| 2xgs | 44P | Uncharacterized protein | / | 0.442 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.442 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.442 | |
| 1ht0 | NAD | Alcohol dehydrogenase 1C | 1.1.1.1 | 0.441 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.441 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.441 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.441 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.441 | |
| 4eph | 0RK | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.441 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.441 | |
| 1tj1 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.440 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.440 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.440 |