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 |
|---|---|---|---|
| 3h0v | M2T | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3h0v | M2T | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 1.000 | |
| 3h0w | N8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.701 | |
| 3dz7 | O8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.680 | |
| 1i7c | MGB | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.654 | |
| 3dz6 | M8E | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.621 | |
| 3dz4 | C8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.605 | |
| 3dz2 | A8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.579 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.501 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.487 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.486 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.486 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.485 | |
| 1i7m | CG | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.484 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.483 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.482 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 3e6e | DCS | Alanine racemase | / | 0.478 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.478 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 2ejz | SAH | Diphthine synthase | / | 0.474 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.473 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.473 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.473 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 1gw2 | FER | Peroxidase C1A | 1.11.1.7 | 0.465 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.464 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.461 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.458 | |
| 4jt8 | 1NR | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.458 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.457 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.456 | |
| 4i10 | 1BS | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.453 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.453 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.452 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.452 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.451 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.449 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.449 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 4wbd | ADP | Putative cysteine ligase BshC | / | 0.448 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.447 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.447 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.446 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.446 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.445 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.444 | |
| 1vfs | DCS | Alanine racemase | / | 0.444 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.444 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1jum | BER | HTH-type transcriptional regulator QacR | / | 0.443 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.443 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.443 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4z87 | GDP | Inosine-5'-monophosphate dehydrogenase | / | 0.443 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 3zdn | FAD | Monoamine oxidase N | 1.4.3.4 | 0.442 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3af0 | GDP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 1dib | L34 | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.440 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 3t4h | MD5 | Alpha-ketoglutarate-dependent dioxygenase AlkB | 1.14.11.33 | 0.440 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4gm4 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.440 |