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 |
|---|---|---|---|
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 1.000 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.630 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.621 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.621 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.600 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.596 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.579 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.558 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.495 | |
| 1gw2 | FER | Peroxidase C1A | 1.11.1.7 | 0.494 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.479 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.478 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.475 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.471 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.471 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.471 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 3ryk | TYD | dTDP-4-dehydrorhamnose 3,5-epimerase | / | 0.469 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.469 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.469 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 1c7o | PPG | Hemolysin | / | 0.466 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.466 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.464 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.464 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.464 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.463 | |
| 3c1o | NAP | Eugenol synthase | / | 0.463 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.462 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.462 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.462 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.461 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.461 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.461 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.459 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.457 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.457 | |
| 4g48 | PZB | Mycocyclosin synthase | 1.14.21.9 | 0.456 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.455 | |
| 4iah | 1DX | Alr2278 protein | / | 0.455 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.454 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.454 | |
| 3eku | CY9 | Actin-5C | / | 0.454 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.454 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.454 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.452 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.452 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.452 | |
| 4iae | 1DX | Alr2278 protein | / | 0.451 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.450 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.450 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.450 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.450 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.450 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.449 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.449 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.448 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.448 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.448 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.447 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2lba | CHO | Fatty acid binding protein 6 | / | 0.446 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.446 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.446 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.445 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.445 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.444 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.444 | |
| 5ero | 210 | Fusicoccadiene synthase | 2.5.1.29 | 0.444 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.443 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.443 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.443 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1lke | DOG | Bilin-binding protein | / | 0.442 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.442 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.442 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3uon | QNB | Muscarinic acetylcholine receptor M2 | / | 0.442 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.441 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.441 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.441 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.440 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 4zow | CLM | Multidrug transporter MdfA | / | 0.440 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.440 |