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 |
|---|---|---|---|
| 3zqa | NDP | NAD/NADP-dependent betaine aldehyde dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3zqa | NDP | NAD/NADP-dependent betaine aldehyde dehydrogenase | / | 1.000 | |
| 2xdr | NDP | NAD/NADP-dependent betaine aldehyde dehydrogenase | / | 0.647 | |
| 2wme | NAP | NAD/NADP-dependent betaine aldehyde dehydrogenase | / | 0.578 | |
| 1bpw | NAD | Betaine aldehyde dehydrogenase | 1.2.1.8 | 0.503 | |
| 4nmj | NAP | Aldehyde dehydrogenase | / | 0.487 | |
| 1o9j | NAD | Aldehyde dehydrogenase, cytosolic 1 | 1.2.1.3 | 0.479 | |
| 2j40 | NAD | 1-pyrroline-5-carboxylate dehydrogenase | / | 0.477 | |
| 3t4n | ADP | 5'-AMP-activated protein kinase subunit gamma | / | 0.472 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.469 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.466 | |
| 4nmk | NAP | Aldehyde dehydrogenase | / | 0.465 | |
| 2bja | NAD | 1-pyrroline-5-carboxylate dehydrogenase | / | 0.464 | |
| 3up0 | D7S | aceDAF-12 | / | 0.464 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.463 | |
| 2j5n | NAD | 1-pyrroline-5-carboxylate dehydrogenase | / | 0.463 | |
| 4l2o | NAD | Aldehyde dehydrogenase, dimeric NADP-preferring | / | 0.461 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.461 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.460 | |
| 3rho | NAP | Cytosolic 10-formyltetrahydrofolate dehydrogenase | 1.5.1.6 | 0.459 | |
| 1uxt | NAD | NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase | / | 0.457 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 3up3 | XCA | aceDAF-12 | / | 0.455 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.454 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.454 | |
| 3w0s | ANP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.453 | |
| 4h73 | NDP | Aldehyde dehydrogenase | / | 0.453 | |
| 4i3w | NAD | Aldehyde dehydrogenase (NAD+) | / | 0.453 | |
| 4m6l | 21V | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.452 | |
| 4i3v | NAD | Aldehyde dehydrogenase (NAD+) | / | 0.451 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.450 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.450 | |
| 1bi9 | NAD | Retinal dehydrogenase 2 | / | 0.449 | |
| 1o02 | NAD | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.449 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.449 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.448 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.448 | |
| 1pn3 | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.448 | |
| 2ay9 | 5PV | Aromatic-amino-acid aminotransferase | 2.6.1.57 | 0.448 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.448 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.448 | |
| 4i8q | NAD | Putative betaine aldehyde dehyrogenase | / | 0.448 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1rt2 | TNK | Gag-Pol polyprotein | 2.7.7.49 | 0.447 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.447 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.447 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.446 | |
| 3czr | 3CZ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.446 | |
| 1lqu | NDP | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.445 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.445 | |
| 4phl | PIL | Phosphodiesterase | / | 0.445 | |
| 4ydu | ADP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.445 | |
| 1a59 | COA | 2-methylcitrate synthase | / | 0.444 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 1ppj | ANY | Cytochrome b | / | 0.444 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.444 | |
| 3iwj | NAD | Aminoaldehyde dehydrogenase | / | 0.444 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.444 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.443 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.443 | |
| 1uxn | NAP | NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase | / | 0.442 | |
| 2ehu | NAD | 1-pyrroline-5-carboxylate dehydrogenase | / | 0.442 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 4ii5 | ADP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 1njf | AGS | DNA polymerase III subunit tau | 2.7.7.7 | 0.441 | |
| 2y6o | 1N1 | Ephrin type-A receptor 4 | 2.7.10.1 | 0.441 | |
| 3n83 | ADP | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.441 | |
| 3vs3 | VSE | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.441 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.441 | |
| 4eqg | A5A | Histidine triad nucleotide-binding protein 1 | 3 | 0.441 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.440 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.440 | |
| 2onm | ADP | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.440 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.440 | |
| 3stv | 3HO | Methylketone synthase I | / | 0.440 | |
| 3vjo | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.440 | |
| 4ddh | MS0 | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.440 | |
| 4x2q | NAD | Retinal dehydrogenase 2 | 1.2.1.36 | 0.440 |