› 2r7b

X-ray diffraction
2.7Å resolution

Crystal Structure of the Phosphoinositide-dependent Kinase-1 (PDK-1)Catalytic Domain bound to a dibenzonaphthyridine inhibitor

Released:
DOI: 10.2210/pdb2r7b/pdb
PDB entry 2r7b coloured by chain, front view.
PDB entry 2r7b coloured by chain, side view.
PDB entry 2r7b coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of dibenzo[c,f][2,7]naphthyridines as potent and selective 3-phosphoinositide-dependent kinase-1 inhibitors.
Gopalsamy A, Shi M, Boschelli DH, Williamson R, Olland A, Hu Y, Krishnamurthy G, Han X, Arndt K, Guo B
J Med Chem 50 5547-9 (2007)
PMID: 17941624

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127511 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-phosphoinositide-dependent protein kinase 1 Chain: A
Molecule details ›
Chain: A
Length: 312 amino acids
Theoretical weight: 35.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O15530 (Residues: 48-359; Coverage: 56%)
Gene names: PDK1, PDPK1
Sequence domains: Protein kinase domain
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand SO4 1 x SO4
Ligand 253 1 x 253
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P3221
Unit cell:
a: 124.281Å b: 124.281Å c: 47.184Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.225 0.225 0.25
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Small-molecule inhibitors of PDK1.
Peifer et al. (2008)
3 more

4 mentions without citation

Qingfei Xiaoyan Wan, a traditional Chinese medicine formula, ameliorates Pseudomonas aeruginosa-induced acute lung inflammation by regulation of PI3K/AKT and Ras/MAPK pathways.
Hou et al. (2016)
3 more