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 |
|---|---|---|---|
| 3o5t | ADP | Nitrogen regulatory protein P-II 1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3o5t | ADP | Nitrogen regulatory protein P-II 1 | / | 1.000 | |
| 2e16 | SAH | Diphthine synthase | / | 0.482 | |
| 2en5 | SAH | Diphthine synthase | / | 0.479 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.474 | |
| 3otf | CMP | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.468 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.467 | |
| 3u9e | COA | Lmo1369 protein | / | 0.467 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.466 | |
| 2pck | SAH | Diphthine synthase | / | 0.464 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.464 | |
| 2q29 | ACO | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.461 | |
| 4qmw | KS1 | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.461 | |
| 2e8q | SAH | Diphthine synthase | / | 0.460 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.460 | |
| 2ejj | SAH | Diphthine synthase | / | 0.459 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.459 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.459 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.458 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.458 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.457 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.457 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.456 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.455 | |
| 4nm9 | FAD | Bifunctional protein PutA | / | 0.455 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.454 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.454 | |
| 4ddh | MS0 | Pantothenate synthetase | 6.3.2.1 | 0.454 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.453 | |
| 1nht | PGS | Adenylosuccinate synthetase | / | 0.453 | |
| 2e7r | SAH | Diphthine synthase | / | 0.453 | |
| 2dsh | SAH | Diphthine synthase | / | 0.452 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2vwh | NAP | Glucose 1-dehydrogenase | / | 0.451 | |
| 3da1 | FAD | Glycerol-3-phosphate dehydrogenase | / | 0.451 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.451 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.450 | |
| 4y35 | F90 | Endothiapepsin | 3.4.23.22 | 0.450 | |
| 1nhq | FAD | NADH peroxidase | 1.11.1.1 | 0.449 | |
| 1z45 | UPG | Bifunctional protein GAL10 | 5.1.3.2 | 0.449 | |
| 2bal | PQA | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 4aa5 | NQB | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 2ed4 | FAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.448 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.448 | |
| 2vht | ATP | NTPase P4 | / | 0.448 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.448 | |
| 4yqf | GDP | Septin-9 | / | 0.448 | |
| 5dp2 | NAP | CurF | / | 0.448 | |
| 1wwk | NAD | 307aa long hypothetical phosphoglycerate dehydrogenase | / | 0.447 | |
| 3elc | F01 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.447 | |
| 3mpt | 1GK | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.446 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.446 | |
| 2gr1 | FAD | Ferredoxin reductase | / | 0.446 | |
| 2q46 | NAP | Uncharacterized protein At5g02240 | / | 0.446 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.446 | |
| 4wct | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.446 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 5cyo | GDP | Septin-9 | / | 0.446 | |
| 2e8h | SAH | Diphthine synthase | / | 0.445 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.445 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.445 | |
| 2huv | SAH | Diphthine synthase | / | 0.445 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.445 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.445 | |
| 3lfm | 3DT | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.445 | |
| 4xgx | ADP | FAD:protein FMN transferase | / | 0.445 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 1t2b | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.444 | |
| 1wng | SAH | Diphthine synthase | / | 0.444 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.444 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.444 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.444 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.444 | |
| 4nu6 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.444 | |
| 1em6 | CP4 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.443 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.443 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.443 | |
| 2w1f | L0F | Aurora kinase A | 2.7.11.1 | 0.443 | |
| 3bkb | STU | Tyrosine-protein kinase Fes/Fps | 2.7.10.2 | 0.443 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.443 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.443 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.443 | |
| 4e5p | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.443 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1qvr | ANP | Chaperone protein ClpB | / | 0.442 | |
| 1sdm | ADP | Kinesin heavy chain-like protein | / | 0.442 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.442 | |
| 3ag6 | PAJ | Pantothenate synthetase | / | 0.442 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 3k5f | AYH | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3v9y | 24L | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.442 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.442 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.441 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.441 | |
| 2egs | SAH | Diphthine synthase | / | 0.441 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.441 | |
| 2pch | SAH | Diphthine synthase | / | 0.441 | |
| 2pvy | ACP | Fibroblast growth factor receptor 2 | / | 0.441 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 4kuh | CAA | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.441 | |
| 4wji | NAP | Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase | / | 0.441 | |
| 1a4i | NDP | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.440 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.440 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1jgt | APC | Carboxyethyl-arginine beta-lactam-synthase | 6.3.3.4 | 0.440 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.440 | |
| 2a87 | FAD | Thioredoxin reductase | 1.8.1.9 | 0.440 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.440 | |
| 2dsi | SAH | Diphthine synthase | / | 0.440 | |
| 2y6o | 1N1 | Ephrin type-A receptor 4 | 2.7.10.1 | 0.440 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.440 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.440 | |
| 4hjo | AQ4 | Epidermal growth factor receptor | 2.7.10.1 | 0.440 | |
| 4p0g | BLG | Membrane-bound lytic murein transglycosylase F | / | 0.440 |