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 |
|---|---|---|---|
| 5c3z | ACP | Ribokinase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 5c3z | ACP | Ribokinase | / | 1.000 | |
| 5c3y | AN2 | Ribokinase | / | 0.660 | |
| 5c41 | ACP | Ribokinase | / | 0.594 | |
| 2aa0 | MTP | Adenosine kinase | 2.7.1.20 | 0.590 | |
| 1lik | ADN | Adenosine kinase | 2.7.1.20 | 0.570 | |
| 1gqt | ACP | Ribokinase | / | 0.544 | |
| 3lki | ATP | Fructokinase | / | 0.541 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.532 | |
| 4e8y | IHA | D-beta-D-heptose 7-phosphate kinase | / | 0.526 | |
| 3nbv | ANP | Ketohexokinase | / | 0.501 | |
| 3q92 | XNB | Ketohexokinase | / | 0.497 | |
| 2f02 | ATP | Tagatose-6-phosphate kinase | / | 0.491 | |
| 3qai | XNN | Ketohexokinase | / | 0.483 | |
| 2hw1 | ANP | Ketohexokinase | / | 0.477 | |
| 3nc9 | TR3 | Ketohexokinase | / | 0.472 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.471 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.471 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.468 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.468 | |
| 3in1 | ADP | Uncharacterized sugar kinase YdjH | 2.7.1 | 0.467 | |
| 4xf7 | ACP | Carbohydrate/pyrimidine kinase, PfkB family | / | 0.467 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.466 | |
| 3qa2 | XNA | Ketohexokinase | / | 0.465 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.464 | |
| 3otx | AP5 | Adenosine kinase, putative | / | 0.463 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.462 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.462 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.461 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.460 | |
| 1pjk | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.458 | |
| 5c40 | ACP | Ribokinase | / | 0.458 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 3nbw | TR4 | Ketohexokinase | / | 0.455 | |
| 2ab8 | ACP | Adenosine kinase | 2.7.1.20 | 0.454 | |
| 3ruq | ADP | Chaperonin | / | 0.454 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.453 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.453 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.453 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1rby | GAR | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.452 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.452 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 1npv | L27 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 1zdw | FLV | Prenyltransferase | / | 0.450 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.450 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 3uqd | ADP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.450 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.448 | |
| 3rus | ADP | Chaperonin | / | 0.447 | |
| 4c0b | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.447 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.447 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.446 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.446 | |
| 1rkd | ADP | Ribokinase | / | 0.445 | |
| 2i5b | ADP | Pyridoxine kinase | / | 0.445 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.445 | |
| 3wfj | NAD | 2-dehydropantoate 2-reductase | / | 0.445 | |
| 1ppj | ANY | Cytochrome b | / | 0.444 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.444 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.444 | |
| 4fv5 | EK9 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.444 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.444 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.443 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.443 | |
| 5itz | LOC | Tubulin beta-2B chain | / | 0.443 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.442 | |
| 3hdm | MMG | Serine/threonine-protein kinase Sgk1 | 2.7.11.1 | 0.442 | |
| 4e8w | IHA | D-beta-D-heptose 7-phosphate kinase | / | 0.442 | |
| 4lj9 | ACP | Chaperone protein ClpB | / | 0.442 | |
| 4mkh | AP5 | Adenylate kinase | / | 0.442 | |
| 1onp | FOM | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.441 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.441 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.441 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.441 | |
| 1d4j | MSC | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 5cvf | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.440 | |
| 5dp2 | NAP | CurF | / | 0.440 |