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 |
|---|---|---|---|
| 3c10 | TSN | Histone deacetylase 7 | 3.5.1.98 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3c10 | TSN | Histone deacetylase 7 | 3.5.1.98 | 1.000 | |
| 3zns | NU7 | Histone deacetylase 7 | 3.5.1.98 | 0.570 | |
| 3znr | NU9 | Histone deacetylase 7 | 3.5.1.98 | 0.557 | |
| 4cby | KEE | Histone deacetylase 4 | 3.5.1.98 | 0.547 | |
| 3c0z | SHH | Histone deacetylase 7 | 3.5.1.98 | 0.546 | |
| 1e92 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.507 | |
| 2vqj | TFG | Histone deacetylase 4 | 3.5.1.98 | 0.495 | |
| 1dgg | NDP | Catalase | 1.11.1.6 | 0.485 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.484 | |
| 4i6h | 1C8 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.483 | |
| 2z52 | H23 | Geranylgeranyl pyrophosphate synthase | / | 0.481 | |
| 4a4l | 939 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.481 | |
| 2xnp | WCX | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.480 | |
| 2e94 | 364 | Geranylgeranyl pyrophosphate synthase | / | 0.479 | |
| 3gcq | 1BU | Mitogen-activated protein kinase 14 | / | 0.478 | |
| 4j52 | 1J3 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.477 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.474 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.474 | |
| 2qhx | FE1 | Pteridine reductase 1 | 1.5.1.33 | 0.473 | |
| 2rku | R78 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.472 | |
| 2w5b | AGS | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.471 | |
| 4a4o | 664 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.471 | |
| 2bfp | H4B | Pteridine reductase 1 | 1.5.1.33 | 0.469 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.468 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.468 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.467 | |
| 2yac | 937 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.467 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.465 | |
| 2ilu | NDP | Lactaldehyde dehydrogenase | 1.2.1.22 | 0.463 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 4a4x | JUP | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.461 | |
| 2bfm | TOP | Pteridine reductase 1 | 1.5.1.33 | 0.459 | |
| 2yee | 2EC | Heat shock protein HSP 90-alpha | / | 0.458 | |
| 3hv3 | R49 | Mitogen-activated protein kinase 14 | / | 0.458 | |
| 3nxy | D2H | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.458 | |
| 4k9y | K9Y | Focal adhesion kinase 1 | 2.7.10.2 | 0.458 | |
| 4ha6 | PXM | Pyridoxine 4-oxidase | / | 0.457 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.456 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.455 | |
| 3l8s | BFF | Mitogen-activated protein kinase 14 | / | 0.455 | |
| 3nxv | D2F | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 2gfs | PQB | Mitogen-activated protein kinase 14 | / | 0.454 | |
| 3ele | PLP | Aminotransferase | / | 0.454 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.454 | |
| 1g3m | PCQ | Estrogen sulfotransferase | 2.8.2.4 | 0.452 | |
| 2avx | HTF | Regulatory protein SdiA | / | 0.451 | |
| 3lfz | ADP | Uncharacterized protein MJ1225 | / | 0.451 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.450 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.450 | |
| 1dgb | NDP | Catalase | 1.11.1.6 | 0.449 | |
| 1vgr | COA | Formyl-CoA:oxalate CoA-transferase | / | 0.449 | |
| 3bjc | WAN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.449 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.449 | |
| 4qx5 | CMP | cGMP-dependent protein kinase 1 | 2.7.11.12 | 0.449 | |
| 1gt5 | BZQ | Odorant-binding protein | / | 0.448 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.448 | |
| 2qqf | A1R | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.448 | |
| 3cth | 319 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.448 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.447 | |
| 2vz0 | D64 | Pteridine reductase | / | 0.447 | |
| 2wky | IBC | Glutamate receptor ionotropic, kainate 1 | / | 0.447 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 1o5r | FR9 | Adenosine deaminase | 3.5.4.4 | 0.446 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.446 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.446 | |
| 3blo | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.446 | |
| 3cv7 | C2U | Alcohol dehydrogenase [NADP(+)] | 1.1.1.2 | 0.446 | |
| 2fk8 | SAM | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.445 | |
| 2pbz | ATP | Uncharacterized protein | / | 0.445 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.445 | |
| 7cat | NDP | Catalase | 1.11.1.6 | 0.445 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 1w19 | T4P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2bfa | CB3 | Pteridine reductase 1 | 1.5.1.33 | 0.444 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.444 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.444 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 2o98 | FSC | 14-3-3-like protein C | / | 0.443 | |
| 2xke | WI2 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.443 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4jqa | ID8 | Aldo-keto reductase family 1 member C2 | / | 0.443 | |
| 5dp2 | NAP | CurF | / | 0.443 | |
| 5p2p | DHG | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.443 | |
| 1i05 | LTL | Major urinary protein 6 | / | 0.442 | |
| 2wqo | VGK | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.442 | |
| 3arp | DEQ | Chitinase A | / | 0.442 | |
| 3pch | CHB | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.442 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.442 | |
| 3uay | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.442 | |
| 4boe | CLR | Japanin | / | 0.442 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.442 | |
| 1kij | NOV | DNA gyrase subunit B | / | 0.441 | |
| 2xnm | WGZ | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.441 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.441 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.441 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 4da8 | BG2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.441 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 5bvw | 1N1 | Epithelial discoidin domain-containing receptor 1 | 2.7.10.1 | 0.441 | |
| 1dr4 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1jtu | LYB | Thymidylate synthase | / | 0.440 | |
| 3bld | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.440 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3e8e | G98 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.440 | |
| 4blc | NDP | Catalase | 1.11.1.6 | 0.440 | |
| 4fa3 | 0SL | Aldo-keto reductase family 1 member C3 | / | 0.440 |