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 |
|---|---|---|---|
| 2vhw | NAI | Alanine dehydrogenase | 1.4.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2vhw | NAI | Alanine dehydrogenase | 1.4.1.1 | 1.000 | |
| 2vhv | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.648 | |
| 2vhx | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.642 | |
| 2vhz | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.633 | |
| 2voj | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.617 | |
| 1ptj | SND | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.504 | |
| 1x7d | NAD | Putative ornithine cyclodeaminase | / | 0.499 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.497 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.492 | |
| 4l4x | NDP | AmphI | / | 0.482 | |
| 5mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.481 | |
| 4wlu | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.480 | |
| 1la2 | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.474 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.473 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.473 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.471 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.471 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.470 | |
| 4ajp | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.470 | |
| 1u28 | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.469 | |
| 1vjt | NAD | Alpha-glucosidase, putative | / | 0.468 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.467 | |
| 1t2d | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.466 | |
| 1l7e | NAI | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.465 | |
| 2oor | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.465 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.464 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.460 | |
| 1hzz | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.457 | |
| 1axe | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.456 | |
| 1pzg | A3D | Lactate dehydrogenase | / | 0.456 | |
| 4xw4 | ANP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.456 | |
| 1nqo | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.455 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.454 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.453 | |
| 3q7d | NPX | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.453 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.452 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.451 | |
| 2fsv | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.451 | |
| 2qfx | NDP | Isocitrate dehydrogenase [NADP], mitochondrial | 1.1.1.42 | 0.451 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.451 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.450 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.450 | |
| 2hjr | APR | Malate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase | / | 0.450 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.450 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.450 | |
| 4oaq | NDP | R-specific carbonyl reductase | / | 0.449 | |
| 1kqo | DND | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.448 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.448 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 4i5c | C5I | Tyrosine-protein kinase JAK1 | / | 0.448 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.448 | |
| 4aos | FAD | Steroid monooxygenase | / | 0.447 | |
| 1ht0 | NAD | Alcohol dehydrogenase 1C | 1.1.1.1 | 0.446 | |
| 1u2d | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.446 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.446 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.446 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.446 | |
| 1hdz | NAD | Alcohol dehydrogenase 1B | 1.1.1.1 | 0.445 | |
| 1u1i | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.445 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.445 | |
| 3qvt | NAI | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.445 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.445 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.444 | |
| 2j4d | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.444 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.444 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.444 | |
| 1lde | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.443 | |
| 4ajo | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.443 | |
| 4gkv | NAD | Alcohol dehydrogenase, propanol-preferring | 1.1.1.1 | 0.443 | |
| 1pzf | A3D | Lactate dehydrogenase | / | 0.442 | |
| 1u2g | APR | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.442 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.442 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.441 | |
| 1r37 | NAD | NAD-dependent alcohol dehydrogenase | 1.1.1.1 | 0.441 | |
| 1rek | B8L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 1wwk | NAD | 307aa long hypothetical phosphoglycerate dehydrogenase | / | 0.441 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.441 | |
| 3m9v | TYD | FAD-dependent oxidoreductase | / | 0.441 | |
| 4yry | NAD | Glutamate synthase, beta subunit | / | 0.441 | |
| 3p0j | TYE | Putative tyrosyl-tRNA synthetase | / | 0.440 | |
| 4kx6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.440 |