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 |
|---|---|---|---|
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 1.000 | |
| 1g38 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.594 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.584 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.547 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.476 | |
| 3qv2 | SAH | 5-cytosine DNA methyltransferase | / | 0.469 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.469 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.469 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.467 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.465 | |
| 4o0r | X4Z | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.463 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.462 | |
| 1s3z | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.459 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.457 | |
| 1osv | CHC | Bile acid receptor | / | 0.457 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.457 | |
| 2b8t | THM | Thymidine kinase | / | 0.454 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.454 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.454 | |
| 4rtl | SFG | DNA adenine methylase | 2.1.1.72 | 0.454 | |
| 2yki | YKI | Heat shock protein HSP 90-alpha | / | 0.453 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.452 | |
| 4gkv | NAD | Alcohol dehydrogenase, propanol-preferring | 1.1.1.1 | 0.452 | |
| 4qms | 1N1 | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.452 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.451 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 4l8u | 9AZ | Serum albumin | / | 0.451 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 1men | GAR | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.450 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.449 | |
| 4eqg | A5A | Histidine triad nucleotide-binding protein 1 | 3 | 0.449 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.448 | |
| 2c0o | L2G | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.448 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3g7j | GTX | Glutathione transferase GST1-4 | / | 0.448 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.448 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.448 | |
| 4jv6 | 18F | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.448 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 3qk0 | QK0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.446 | |
| 1reo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.445 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.445 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4g6h | NAI | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.445 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.445 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.444 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.444 | |
| 2ww4 | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.444 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.444 | |
| 4a33 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.444 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.443 | |
| 2h3w | COA | Carnitine O-acetyltransferase | 2.3.1.7 | 0.443 | |
| 3o6o | 94M | Heat shock protein 83 | / | 0.443 | |
| 3te4 | ACO | Dopamine N-acetyltransferase | / | 0.443 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 1uy9 | PU6 | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.442 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.442 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.442 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.441 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.441 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.441 | |
| 2ozu | ACO | Histone acetyltransferase KAT6A | / | 0.440 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 3hdm | MMG | Serine/threonine-protein kinase Sgk1 | 2.7.11.1 | 0.440 | |
| 4do3 | 0LA | Fatty-acid amide hydrolase 1 | 3.5.1.99 | 0.440 |