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 |
|---|---|---|---|
| 3vax | PLP | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3vax | PLP | Uncharacterized protein | / | 1.000 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.477 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.469 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.468 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.466 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.463 | |
| 3vxj | 3DM | DyP | / | 0.461 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.460 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.460 | |
| 4qxp | 1YE | Stimulator of interferon genes protein | / | 0.459 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.458 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.457 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.457 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.456 | |
| 3gwd | NAP | Cyclohexanone monooxygenase | / | 0.456 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.456 | |
| 3fui | 812 | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.455 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.454 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.454 | |
| 4c13 | UML | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase | / | 0.454 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.453 | |
| 1eyy | NAP | NADP-dependent fatty aldehyde dehydrogenase | 1.2.1.4 | 0.452 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.450 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.450 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.450 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.450 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.450 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.449 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.448 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.448 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.448 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.448 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.447 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.447 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.447 | |
| 1o01 | NAD | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.446 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.446 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4dk7 | 0KS | Oxysterols receptor LXR-beta | / | 0.446 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.446 | |
| 5dn1 | AMZ | Phosphoribosyl isomerase A | 5.3.1.16 | 0.446 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.445 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.445 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2x8h | FAD | Thioredoxin glutathione reductase | / | 0.445 | |
| 3t94 | MTA | S-methyl-5'-thioadenosine phosphorylase | / | 0.445 | |
| 2ilv | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.444 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.444 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.443 | |
| 2a7r | 5GP | GMP reductase 2 | / | 0.443 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 3fpj | SAM | Uncharacterized protein | / | 0.443 | |
| 3h2s | NDP | Putative NADH-flavin reductase | / | 0.443 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.443 | |
| 4c77 | N01 | Phenylacetone monooxygenase | 1.14.13.92 | 0.443 | |
| 5d4v | YGP | Uncharacterized protein MJ0489 | / | 0.443 | |
| 1i5c | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.442 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.442 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.442 | |
| 2i7p | ACO | Pantothenate kinase 3 | 2.7.1.33 | 0.442 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.442 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.442 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.442 | |
| 3te4 | ACO | Dopamine N-acetyltransferase | / | 0.442 | |
| 1i6x | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.441 | |
| 1nhq | FAD | NADH peroxidase | 1.11.1.1 | 0.441 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.441 | |
| 2f3f | AXF | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.441 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.441 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.441 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.441 | |
| 4lz8 | 1YX | Glutamate receptor 2 | / | 0.441 | |
| 1x27 | ASP_TYR_VAL_HIS_PTR | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.440 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.440 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.440 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.440 | |
| 3img | BZ3 | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 4eph | 0RK | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.440 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.440 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.440 |