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 |
|---|---|---|---|
| 1qay | MEV | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1qay | MEV | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 1.000 | |
| 1qax | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.628 | |
| 4i4b | 1CV | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.550 | |
| 1t02 | LVA | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.484 | |
| 3ijd | C2F | Methylenetetrahydrofolate reductase | / | 0.476 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.473 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.469 | |
| 2q0l | FAD | Thioredoxin reductase | 1.8.1.9 | 0.467 | |
| 2itq | ITQ | Epidermal growth factor receptor | 2.7.10.1 | 0.466 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.466 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 1dq9 | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.34 | 0.464 | |
| 4qys | PLR | Tryptophan synthase beta chain 2 | 4.2.1.20 | 0.464 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.461 | |
| 1j7k | ATP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.459 | |
| 3fro | NHF | GlgA glycogen synthase | / | 0.459 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.459 | |
| 1pzh | NAD | Lactate dehydrogenase | / | 0.458 | |
| 2c3i | IYZ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.458 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.458 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.458 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.458 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.457 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.456 | |
| 5dr2 | ATP | Aurora kinase A | 2.7.11.1 | 0.456 | |
| 3kga | LX9 | MAP kinase-activated protein kinase 2 | 2.7.11.1 | 0.455 | |
| 4fhf | 0TT | Spore photoproduct lyase | / | 0.455 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.454 | |
| 1hk5 | T44 | Serum albumin | / | 0.452 | |
| 3dd1 | 25D | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.452 | |
| 1qf5 | RPL | Adenylosuccinate synthetase | / | 0.451 | |
| 1wwk | NAD | 307aa long hypothetical phosphoglycerate dehydrogenase | / | 0.451 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.450 | |
| 3qf9 | NM8 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.450 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 2nu9 | COA | Succinate--CoA ligase [ADP-forming] subunit alpha | 6.2.1.5 | 0.449 | |
| 3a20 | FMN | FMN-binding protein | / | 0.449 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.449 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.448 | |
| 2oj9 | BMI | Insulin-like growth factor 1 receptor | 2.7.10.1 | 0.448 | |
| 3t54 | ATP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.448 | |
| 1g69 | TZP | Thiamine-phosphate synthase | / | 0.447 | |
| 1i8t | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.447 | |
| 2b1p | AIZ | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.447 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.447 | |
| 2wd9 | IBP | Acyl-coenzyme A synthetase ACSM2A, mitochondrial | 6.2.1.2 | 0.447 | |
| 3vn2 | TLS | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.447 | |
| 1bof | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.446 | |
| 2exc | JNK | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.446 | |
| 2gmj | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.446 | |
| 2idk | C2F | Glycine N-methyltransferase | 2.1.1.20 | 0.446 | |
| 3hx4 | ANP | Calmodulin-domain protein kinase 1 | / | 0.446 | |
| 4c4g | 7RO | Dual specificity protein kinase TTK | 2.7.12.1 | 0.446 | |
| 4otw | DB8 | Receptor tyrosine-protein kinase erbB-3 | 2.7.10.1 | 0.446 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.445 | |
| 2zdt | 46C | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.445 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.445 | |
| 2gtk | 208 | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.444 | |
| 3c15 | FOK | Adenylate cyclase type 2 | / | 0.444 | |
| 3c15 | FOK | Adenylate cyclase type 5 | / | 0.444 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.444 | |
| 3unj | 0BX | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 4qmz | B49 | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.444 | |
| 3b89 | 5GP | 16S rRNA methylase | / | 0.443 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.443 | |
| 3dme | FAD | Putative conserved exported protein | / | 0.443 | |
| 4at4 | T6E | BDNF/NT-3 growth factors receptor | 2.7.10.1 | 0.443 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.442 | |
| 2xh9 | J01 | Uncharacterized protein | / | 0.442 | |
| 3da1 | FAD | Glycerol-3-phosphate dehydrogenase | / | 0.442 | |
| 3el9 | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.442 | |
| 3rsr | N5P | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.442 | |
| 4l9y | 1VU | L-malyl-CoA/beta-methylmalyl-CoA lyase | 4.1.3.24 | 0.442 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.442 | |
| 1qvn | FRI | Interleukin-2 | / | 0.441 | |
| 1unl | RRC | Cyclin-dependent-like kinase 5 | 2.7.11.1 | 0.441 | |
| 2bhi | SFT | Cytotoxin 3 | / | 0.441 | |
| 3efw | AK8 | Aurora kinase A | 2.7.11.1 | 0.441 | |
| 3r7c | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.441 | |
| 3ruv | ANP | Chaperonin | / | 0.441 | |
| 4gmy | 0X5 | Tyrosine-protein kinase JAK2 | / | 0.441 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 5a3b | APR | SIR2 family protein | / | 0.441 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.440 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.440 | |
| 2q6c | HR1 | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.34 | 0.440 | |
| 3ocp | CMP | cGMP-dependent protein kinase 1 | 2.7.11.12 | 0.440 | |
| 3ruq | ADP | Chaperonin | / | 0.440 | |
| 4bdh | WVI | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.440 | |
| 4g1w | G1W | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.440 | |
| 4n4v | 2GY | Tankyrase-1 | 2.4.2.30 | 0.440 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.440 | |
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 | 0.440 |