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 |
|---|---|---|---|
| 3dz2 | A8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3dz2 | A8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 1.000 | |
| 3dz4 | C8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.778 | |
| 3dz6 | M8E | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.767 | |
| 3dz7 | O8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.678 | |
| 3h0w | N8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.645 | |
| 3h0v | M2T | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.559 | |
| 1i7m | CG | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.528 | |
| 1i7c | MGB | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.520 | |
| 2ejz | SAH | Diphthine synthase | / | 0.497 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.490 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.483 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.474 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.473 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.470 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.469 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.467 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.466 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.466 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.459 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.458 | |
| 3zov | WZV | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.455 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.455 | |
| 4axa | RKD | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.455 | |
| 2ilv | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.454 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.454 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.454 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.454 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.449 | |
| 3qgi | 33F | Genome polyprotein | 2.7.7.48 | 0.449 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.448 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.447 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.446 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.446 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.446 | |
| 4xrg | NAD | Homospermidine synthase | 2.5.1.44 | 0.446 | |
| 1c7o | PPG | Hemolysin | / | 0.445 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 3e6e | DCS | Alanine racemase | / | 0.445 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.445 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.444 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.444 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4hb9 | FAD | Uncharacterized protein | / | 0.444 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.443 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 4c2z | 646 | Glycylpeptide N-tetradecanoyltransferase 1 | / | 0.443 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.442 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.442 | |
| 1fw0 | KAI | Glutamate receptor 2 | / | 0.441 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.440 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.440 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 4i10 | 1BS | Beta-secretase 1 | 3.4.23.46 | 0.440 |