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 |
|---|---|---|---|
| 2cbr | A80 | Cellular retinoic acid-binding protein 1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2cbr | A80 | Cellular retinoic acid-binding protein 1 | / | 1.000 | |
| 1cbr | REA | Cellular retinoic acid-binding protein 1 | / | 0.563 | |
| 1cbq | RE9 | Cellular retinoic acid-binding protein 2 | / | 0.533 | |
| 1cbs | REA | Cellular retinoic acid-binding protein 2 | / | 0.530 | |
| 2g78 | REA | Cellular retinoic acid-binding protein 2 | / | 0.530 | |
| 2cbs | R13 | Cellular retinoic acid-binding protein 2 | / | 0.509 | |
| 3cbs | R12 | Cellular retinoic acid-binding protein 2 | / | 0.509 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.482 | |
| 2fr3 | REA | Cellular retinoic acid-binding protein 2 | / | 0.471 | |
| 3cwk | REA | Cellular retinoic acid-binding protein 2 | / | 0.471 | |
| 5dp2 | NAP | CurF | / | 0.469 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.468 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.466 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.464 | |
| 3eks | CY9 | Actin-5C | / | 0.463 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.463 | |
| 3vw7 | VPX | Proteinase-activated receptor 1 | / | 0.462 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.461 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.460 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.460 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.459 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.458 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.457 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4rls | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.456 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.454 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.454 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.454 | |
| 3pm9 | FAD | Putative oxidoreductase | / | 0.454 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.454 | |
| 2w2l | NAD | D-mandelate dehydrogenase | / | 0.453 | |
| 2zno | S44 | Peroxisome proliferator-activated receptor gamma | / | 0.453 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.452 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.452 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.452 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.452 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.451 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.451 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.451 | |
| 1khr | COA | Streptogramin A acetyltransferase | 2.3.1 | 0.450 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.450 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.450 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.450 | |
| 4ien | COA | Putative acyl-CoA hydrolase | / | 0.450 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.450 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3iaa | TYD | CalG2 | / | 0.449 | |
| 3ieu | GDP | GTPase Era | / | 0.449 | |
| 1kfb | IGP | Tryptophan synthase alpha chain | / | 0.448 | |
| 2ejz | SAH | Diphthine synthase | / | 0.448 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.448 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.448 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.448 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.448 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.448 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.448 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.448 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.447 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.447 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.447 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.447 | |
| 4a31 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.447 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.446 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.445 | |
| 4nu5 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.445 | |
| 5ikr | ID8 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.445 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.444 | |
| 1jed | ADP | Sulfate adenylyltransferase | / | 0.443 | |
| 1mr9 | ACO | Streptogramin A acetyltransferase | 2.3.1 | 0.443 | |
| 1q20 | PLO | Sulfotransferase family cytosolic 2B member 1 | 2.8.2.2 | 0.443 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.443 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.443 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.443 | |
| 4qec | NAP | ElxO | / | 0.443 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.442 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.442 | |
| 1pnv | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.442 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.442 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.442 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.442 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.442 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.442 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.441 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.441 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.441 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.441 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3ntr | NAD | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.441 | |
| 3vey | 0H5 | Glucokinase | 2.7.1.2 | 0.441 | |
| 5kjc | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.440 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.440 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.440 |