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 |
|---|---|---|---|
| 3cmp | EB4 | Neutrophil gelatinase-associated lipocalin |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3cmp | EB4 | Neutrophil gelatinase-associated lipocalin | / | 1.000 | |
| 3cmp | DBH | Neutrophil gelatinase-associated lipocalin | / | 0.537 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.504 | |
| 2qx7 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.495 | |
| 1ryw | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.492 | |
| 2cah | NDP | Catalase | 1.11.1.6 | 0.492 | |
| 1szc | CNA | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.491 | |
| 4xyb | NDP | Formate dehydrogenase | / | 0.488 | |
| 2xpv | MIY | Tetracycline repressor protein class D | / | 0.486 | |
| 3kqj | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.479 | |
| 3vcy | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.479 | |
| 4e37 | NDP | Catalase | 1.11.1.6 | 0.479 | |
| 2eud | GCQ | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.478 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 2vax | CSC | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.471 | |
| 4biz | ADP | Sensor histidine kinase CpxA | / | 0.471 | |
| 4c77 | N01 | Phenylacetone monooxygenase | 1.14.13.92 | 0.467 | |
| 2imk | GTX | AGAP009194-PA | / | 0.466 | |
| 2r6j | NDP | Eugenol synthase 1 | 1.1.1.318 | 0.466 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.465 | |
| 1nlm | UD1 | UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase | / | 0.464 | |
| 2ax4 | ADP | Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 | 2.7.1.25 | 0.464 | |
| 2w2l | NAD | D-mandelate dehydrogenase | / | 0.464 | |
| 1gox | FMN | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.462 | |
| 2rl1 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.462 | |
| 3ed1 | GA3 | Gibberellin receptor GID1 | / | 0.462 | |
| 3gol | XND | Genome polyprotein | 2.7.7.48 | 0.462 | |
| 1equ | EQI | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.461 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.460 | |
| 4aux | XTC | Tetracycline repressor protein class D | / | 0.460 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.460 | |
| 2x86 | ADP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.459 | |
| 3hpq | AP5 | Adenylate kinase | / | 0.459 | |
| 1n5t | OAL | ActVA 6 protein | / | 0.458 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.457 | |
| 4f1y | CNI | Glutamate receptor 3 | / | 0.457 | |
| 4uz6 | SCR | Palmitoleoyl-protein carboxylesterase NOTUM | / | 0.457 | |
| 4xr9 | TMP | CalS8 | / | 0.457 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.457 | |
| 3gnw | XNC | Genome polyprotein | 2.7.7.48 | 0.456 | |
| 1f3p | FAD | Ferredoxin reductase | / | 0.455 | |
| 1g9b | BAB | Botulinum neurotoxin type B | 3.4.24.69 | 0.455 | |
| 1q3g | UDA | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.455 | |
| 4at4 | T6E | BDNF/NT-3 growth factors receptor | 2.7.10.1 | 0.455 | |
| 4isu | IKM | Glutamate receptor 2 | / | 0.455 | |
| 1i2c | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.454 | |
| 4bqy | FNT | Egl nine homolog 1 | / | 0.454 | |
| 1u1d | 181 | Uridine phosphorylase | 2.4.2.3 | 0.453 | |
| 2bn4 | NAP | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.452 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.451 | |
| 1ja1 | NAP | NADPH--cytochrome P450 reductase | / | 0.450 | |
| 2bue | COA | AAC(6')-Ib | / | 0.450 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 3cvy | FAD | RE11660p | / | 0.450 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3v4t | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.450 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.449 | |
| 1w29 | TS0 | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.449 | |
| 4ie0 | PD2 | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.449 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 1qrr | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.448 | |
| 2cdu | FAD | NADH oxidase | / | 0.448 | |
| 2r2l | PB9 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.448 | |
| 3b7d | CNI | Glutamate receptor 2 | / | 0.448 | |
| 3iss | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.448 | |
| 3koq | FMN | Putative nitroreductase | / | 0.448 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.447 | |
| 4loh | 1SY | Stimulator of interferon genes protein | / | 0.447 | |
| 2a19 | ANP | Interferon-induced, double-stranded RNA-activated protein kinase | 2.7.11.1 | 0.446 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.446 | |
| 2yvw | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.446 | |
| 4bzq | ADP | Bifunctional enzyme CysN/CysC | 2.7.1.25 | 0.446 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.446 | |
| 1i4l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.445 | |
| 2e0a | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.445 | |
| 2xau | ADP | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 | 3.6.4.13 | 0.445 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.445 | |
| 1osv | CHC | Bile acid receptor | / | 0.444 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2cbs | R13 | Cellular retinoic acid-binding protein 2 | / | 0.444 | |
| 3ebl | GA4 | Gibberellin receptor GID1 | / | 0.444 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 3lpf | Z77 | Beta-glucuronidase | 3.2.1.31 | 0.444 | |
| 3lth | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.444 | |
| 3nf8 | CDQ | Gag-Pol polyprotein | / | 0.444 | |
| 4b65 | NDP | L-ornithine N(5)-monooxygenase | / | 0.444 | |
| 4fdp | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.444 | |
| 4lis | UPG | UDP-glucose 4-epimerase (Eurofung) | / | 0.444 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4g0k | 0VS | Glutathionyl-hydroquinone reductase YqjG | 1.8 | 0.443 | |
| 1dgb | NDP | Catalase | 1.11.1.6 | 0.442 | |
| 1l2o | ADP | Myosin heavy chain, striated muscle | / | 0.442 | |
| 2lbv | EB4 | Extracellular fatty acid-binding protein | / | 0.442 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.442 | |
| 3af2 | ACP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3kp0 | Z98 | D-ornithine 4,5-aminomutase subunit beta | / | 0.442 | |
| 3od4 | 8XQ | Hypoxia-inducible factor 1-alpha inhibitor | 1.14.11.30 | 0.442 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.442 | |
| 4nhy | PD2 | Prolyl 3-hydroxylase OGFOD1 | 1.14.11 | 0.442 | |
| 3zzh | NLG | Protein ARG5,6, mitochondrial | 2.7.2.8 | 0.441 | |
| 4iz0 | 2BI | Genome polyprotein | 2.7.7.48 | 0.441 | |
| 4yp1 | 2BA | Stimulator of interferon genes protein | / | 0.441 | |
| 1pnq | NDP | NAD(P) transhydrogenase subunit beta | 1.6.1.2 | 0.440 | |
| 2b9x | FAD | Putative aminooxidase | / | 0.440 | |
| 3h5s | H5S | Genome polyprotein | 2.7.7.48 | 0.440 | |
| 3ksl | SZH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 3rha | FDA | Putrescine oxidase | / | 0.440 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.440 | |
| 3zo7 | K6H | Muconolactone Delta-isomerase | / | 0.440 | |
| 5iw4 | NAD | NADH pyrophosphatase | / | 0.440 |