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 |
|---|---|---|---|
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 1.000 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.517 | |
| 4yuv | S4M | Spermidine synthase, putative | / | 0.515 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.500 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.491 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.489 | |
| 4tvb | NAD | Homospermidine synthase | 2.5.1.44 | 0.485 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.477 | |
| 2rew | REW | Peroxisome proliferator-activated receptor alpha | / | 0.473 | |
| 1dfo | FFO | Serine hydroxymethyltransferase | 2.1.2.1 | 0.472 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.471 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.464 | |
| 3cgb | COA | Coenzyme A disulfide reductase | / | 0.462 | |
| 2ww4 | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.461 | |
| 2vhw | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.459 | |
| 4yv0 | S4M | Spermidine synthase, putative | / | 0.457 | |
| 3e8e | G98 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.456 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.455 | |
| 1k6v | XN2 | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.453 | |
| 1trb | FAD | Thioredoxin reductase | 1.8.1.9 | 0.451 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.451 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.450 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.448 | |
| 1tdf | FAD | Thioredoxin reductase | 1.8.1.9 | 0.447 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.447 | |
| 3elc | F01 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.446 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.445 | |
| 1tde | FAD | Thioredoxin reductase | 1.8.1.9 | 0.444 | |
| 1xwf | ADN | Adenosylhomocysteinase | 3.3.1.1 | 0.444 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.444 | |
| 1mei | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.443 | |
| 2aa0 | MTP | Adenosine kinase | 2.7.1.20 | 0.443 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.443 | |
| 3qv2 | SAH | 5-cytosine DNA methyltransferase | / | 0.443 | |
| 4hy6 | FJ1 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 4m11 | MXM | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.443 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.442 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.442 | |
| 3fwr | ADP | Transcriptional repressor CcpN | / | 0.441 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.441 | |
| 3tdj | 3TJ | Glutamate receptor 2 | / | 0.441 | |
| 4e4q | RRH | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.441 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.440 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.440 | |
| 4axa | RKD | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 4e5m | NAP | Phosphonate dehydrogenase | 1.20.1.1 | 0.440 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.440 |