sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4du6 | GTP | GTP cyclohydrolase 1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4du6 | GTP | GTP cyclohydrolase 1 | / | 1.000 | |
| 1a9c | GTP | GTP cyclohydrolase 1 | 3.5.4.16 | 0.565 | |
| 1a8r | GTP | GTP cyclohydrolase 1 | 3.5.4.16 | 0.509 | |
| 1n3r | GTP | GTP cyclohydrolase 1 | 3.5.4.16 | 0.494 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.481 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.476 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.474 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.470 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.470 | |
| 1wur | 8DG | GTP cyclohydrolase 1 | / | 0.466 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.466 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.465 | |
| 5dp2 | NAP | CurF | / | 0.460 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.459 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.459 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.458 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.458 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.457 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.457 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.457 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.456 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.456 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.455 | |
| 3jzi | JZL | Biotin carboxylase | 6.3.4.14 | 0.455 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.455 | |
| 4a2a | ATP | Cell division protein FtsA | / | 0.455 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.454 | |
| 1ozp | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.453 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.451 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.451 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.451 | |
| 4gyy | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.451 | |
| 2a2c | ADP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.450 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.450 | |
| 2wya | HMG | Hydroxymethylglutaryl-CoA synthase, mitochondrial | 2.3.3.10 | 0.450 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.450 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.449 | |
| 2r8o | T5X | Transketolase 1 | / | 0.449 | |
| 3daa | PDD | D-alanine aminotransferase | 2.6.1.21 | 0.449 | |
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.449 | |
| 3uov | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.449 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.449 | |
| 1wua | AP8 | Actin, alpha skeletal muscle | / | 0.448 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.448 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.448 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.447 | |
| 3bw2 | FMN | Putative 2-nitropropane dioxygenase | / | 0.447 | |
| 3csc | ACO | Citrate synthase, mitochondrial | 2.3.3.1 | 0.446 | |
| 3ieu | GDP | GTPase Era | / | 0.446 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.446 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.445 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.445 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.445 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.445 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.445 | |
| 4to5 | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.445 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.445 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.444 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.444 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.444 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.444 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.444 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1qyw | 5SD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 2hej | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.443 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.443 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.443 | |
| 4qfy | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.443 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.443 | |
| 4zwe | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.443 | |
| 1kw8 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.442 | |
| 3gwd | NAP | Cyclohexanone monooxygenase | / | 0.442 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.441 | |
| 4dk7 | 0KS | Oxysterols receptor LXR-beta | / | 0.441 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.441 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.441 | |
| 5cts | CMC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.441 | |
| 1cbr | REA | Cellular retinoic acid-binding protein 1 | / | 0.440 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.440 | |
| 4jay | NAP | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.440 | |
| 4to4 | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.440 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.440 |