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 |
|---|---|---|---|
| 4inb | 1F6 | Gag protein |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4inb | 1F6 | Gag protein | / | 1.000 | |
| 2hqp | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.494 | |
| 1eup | ASD | 6-deoxyerythronolide B hydroxylase | / | 0.475 | |
| 4c4j | X21 | Dual specificity protein kinase TTK | 2.7.12.1 | 0.474 | |
| 1mb9 | ATP | Carboxyethyl-arginine beta-lactam-synthase | 6.3.3.4 | 0.472 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.472 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.468 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.467 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.467 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.467 | |
| 4elg | 52J | Dihydrofolate reductase | / | 0.464 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.463 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.461 | |
| 2go4 | TUX | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.461 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.461 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.461 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.460 | |
| 2dub | CO8 | Enoyl-CoA hydratase, mitochondrial | 4.2.1.17 | 0.460 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.460 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.460 | |
| 3h1j | SMA | Cytochrome b | / | 0.460 | |
| 4oze | 24G | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.460 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.459 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3wdl | ATP | 4-phosphopantoate--beta-alanine ligase | 6.3.2.36 | 0.459 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.458 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.457 | |
| 1soz | VAL_TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.455 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.455 | |
| 4d0l | 093 | Phosphatidylinositol 4-kinase beta | 2.7.1.67 | 0.455 | |
| 4f9m | FCM | Peroxisome proliferator-activated receptor gamma | / | 0.455 | |
| 4i3w | NAD | Aldehyde dehydrogenase (NAD+) | / | 0.455 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.454 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.454 | |
| 3c6u | M22 | Gag-Pol polyprotein | 2.7.7.49 | 0.454 | |
| 4m10 | ICD | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.454 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.454 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2prh | 238 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.453 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.453 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 4eev | L1X | Hepatocyte growth factor receptor | 2.7.10.1 | 0.452 | |
| 4g48 | PZB | Mycocyclosin synthase | 1.14.21.9 | 0.452 | |
| 1d3h | A26 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.451 | |
| 2ath | 3EA | Peroxisome proliferator-activated receptor gamma | / | 0.451 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.451 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.451 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.451 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.450 | |
| 2q66 | ATP | Poly(A) polymerase | 2.7.7.19 | 0.450 | |
| 3zbn | COA | 3-ketoacyl-CoA thiolase-like protein | / | 0.450 | |
| 1ppj | ANY | Cytochrome b | / | 0.449 | |
| 2nnh | REA | Cytochrome P450 2C8 | / | 0.449 | |
| 2xb5 | I7T | Tetracycline repressor protein class D | / | 0.449 | |
| 4eqw | FAD | Coenzyme A disulfide reductase | / | 0.449 | |
| 2a0c | CK9 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.448 | |
| 3pe6 | ZYH | Monoglyceride lipase | / | 0.448 | |
| 4k2x | FAD | Polyketide oxygenase/hydroxylase | / | 0.448 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.448 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.448 | |
| 1knu | YPA | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 1ml6 | GBX | Glutathione S-transferase A2 | 2.5.1.18 | 0.447 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.447 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.447 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.447 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.447 | |
| 1e7a | PFL | Serum albumin | / | 0.446 | |
| 1iwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.446 | |
| 4a9m | P9M | Bromodomain-containing protein 2 | / | 0.446 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.446 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 3h6k | 33T | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 4h3c | 0YZ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.445 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.445 | |
| 1sn5 | T3 | Transthyretin | / | 0.444 | |
| 1z1f | STL | Resveratrol synthase | / | 0.444 | |
| 2o3z | AI7 | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.444 | |
| 2q8s | L92 | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 3p6m | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.444 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.444 | |
| 4jaz | STL | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 4ubs | DIF | Pentalenic acid synthase | 1.14.15.11 | 0.444 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.444 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.443 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.443 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.442 | |
| 1fm9 | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.442 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 3cyl | VIT | Basic phospholipase A2 homolog piratoxin-2 | / | 0.442 | |
| 3vn2 | TLS | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 3zuy | TCH | Transporter | / | 0.442 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.442 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.442 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.442 | |
| 4xuh | SFI | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.441 | |
| 1m9k | 7NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.441 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.441 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.441 | |
| 2p33 | J07 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.441 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.441 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3pgq | GY3 | Acetyl-CoA carboxylase | / | 0.441 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.441 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.441 | |
| 4ph9 | IBP | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.441 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1gyp | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.440 | |
| 1rbm | KT5 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.440 | |
| 2qk8 | MTX | Dihydrofolate reductase | / | 0.440 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 3gob | HXX | DdmC | / | 0.440 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.440 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.440 | |
| 3wd7 | COA | Acridone synthase | / | 0.440 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.440 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 5eyp | LOC | Tubulin beta chain | / | 0.440 |