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 |
|---|---|---|---|
| 2e7z | MGD | Acetylene hydratase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2e7z | MGD | Acetylene hydratase | / | 1.000 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.484 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.477 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.475 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.474 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.473 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.469 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.468 | |
| 4u0m | GTP | Cyclic GMP-AMP synthase | / | 0.468 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.466 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.466 | |
| 3eyh | IZA | Tyrosine-protein kinase JAK1 | / | 0.464 | |
| 4brd | ANP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.464 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.464 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.464 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.463 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.463 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.462 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.461 | |
| 4lb2 | DM5 | Serum albumin | / | 0.459 | |
| 1l8q | ADP | Chromosomal replication initiator protein DnaA | / | 0.457 | |
| 4prx | ADP | DNA gyrase subunit B | / | 0.457 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.456 | |
| 3lxp | IZA | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.456 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.456 | |
| 4fod | 0UV | ALK tyrosine kinase receptor | 2.7.10.1 | 0.455 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.455 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.455 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.452 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 1l4m | NCN | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | 2.4.2.21 | 0.451 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1y57 | MPZ | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.451 | |
| 2y3s | TIR | TamL | / | 0.451 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.450 | |
| 1tl7 | FOK | Adenylate cyclase type 2 | / | 0.449 | |
| 1tl7 | FOK | Adenylate cyclase type 5 | / | 0.449 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.448 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.448 | |
| 3uqd | ADP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.448 | |
| 2y4g | TIR | TamL | / | 0.447 | |
| 3pm4 | F5N | Endothiapepsin | 3.4.23.22 | 0.447 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.446 | |
| 4hj4 | FMN | LOV protein | / | 0.446 | |
| 5dp2 | NAP | CurF | / | 0.446 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3dv3 | MEK | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.445 | |
| 3m2r | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.445 | |
| 3m2r | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.445 | |
| 4hia | FMN | LOV protein | / | 0.445 | |
| 4mgi | CMP | Rap guanine nucleotide exchange factor 4 | / | 0.445 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.444 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.444 | |
| 4imf | SI3 | N-acetylneuraminate lyase | / | 0.444 | |
| 4y3j | HIC | Endothiapepsin | 3.4.23.22 | 0.444 | |
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 | 0.443 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.443 | |
| 2p9d | SAH | Diphthine synthase | / | 0.443 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.443 | |
| 3mkn | DNB | Pyrimidine-specific ribonucleoside hydrolase RihB | / | 0.443 | |
| 3p0h | FSE | Putative tyrosyl-tRNA synthetase | / | 0.443 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.443 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.443 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 2bxq | IMN | Serum albumin | / | 0.442 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.442 | |
| 2huq | SAH | Diphthine synthase | / | 0.442 | |
| 2v9j | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.442 | |
| 4fv7 | E94 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.442 | |
| 4xzm | NAP | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.442 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.441 | |
| 3lfm | 3DT | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.441 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.441 | |
| 3o0q | ADN | Vitamin B12-dependent ribonucleotide reductase | / | 0.441 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.441 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.441 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.441 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.440 | |
| 1i6k | TYM | Tryptophan--tRNA ligase | 6.1.1.2 | 0.440 | |
| 1kvk | ATP | Mevalonate kinase | 2.7.1.36 | 0.440 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 2bxm | IMN | Serum albumin | / | 0.440 | |
| 2cgp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.440 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.440 | |
| 2q46 | NAP | Uncharacterized protein At5g02240 | / | 0.440 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.440 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.440 | |
| 4ehu | ANP | 2-hydroxyisocaproyl-CoA dehydratase activator | / | 0.440 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.440 |