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 |
|---|---|---|---|
| 1xgi | NST | Beta-lactamase | 3.5.2.6 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1xgi | NST | Beta-lactamase | 3.5.2.6 | 1.000 | |
| 2r9x | WH6 | Beta-lactamase | 3.5.2.6 | 0.639 | |
| 1xgj | HTC | Beta-lactamase | 3.5.2.6 | 0.634 | |
| 2r9w | 23C | Beta-lactamase | 3.5.2.6 | 0.560 | |
| 2pu2 | DK2 | Beta-lactamase | 3.5.2.6 | 0.523 | |
| 3gtc | GTC | Beta-lactamase | 3.5.2.6 | 0.493 | |
| 1l2s | STC | Beta-lactamase | 3.5.2.6 | 0.479 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.477 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.475 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.471 | |
| 4e2d | FMN | Dehydrogenase | / | 0.467 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.466 | |
| 2hpv | FMN | FMN-dependent NADH-azoreductase | 1.7 | 0.464 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.456 | |
| 2zyn | BCD | Periplasmic binding protein | / | 0.455 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.454 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.453 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.452 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.449 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.448 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.448 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.448 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.448 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.447 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.447 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.446 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.446 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.445 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.444 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.444 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.444 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.443 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.443 | |
| 3own | 3OX | Renin | 3.4.23.15 | 0.443 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.443 | |
| 1dyh | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3c3e | GDP | 2-phospho-L-lactate transferase | / | 0.442 | |
| 5a3b | APR | SIR2 family protein | / | 0.442 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.441 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.441 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.441 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.441 | |
| 1d4d | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.440 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.440 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.440 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.440 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.440 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.440 |