› 2pe0

X-ray diffraction
2.35Å resolution

CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) 5-Hydroxy-3-[1-(1H-pyrrol-2-yl)-eth-(Z)-ylidene]-1,3-dihydro-indol-2-one COMPLEX

Released:
DOI: 10.2210/pdb2pe0/pdb
PDB entry 2pe0 coloured by chain, front view.
PDB entry 2pe0 coloured by chain, side view.
PDB entry 2pe0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors. Part 1: design, synthesis and biological activity.
Islam I, Bryant J, Chou YL, Kochanny MJ, Lee W, Phillips GB, Yu H, Adler M, Whitlow M, Ho E, Lentz D, Polokoff MA, Subramanyam B, Wu JM, Zhu D, Feldman RI, Arnaiz DO
Bioorg Med Chem Lett 17 3814-8 (2007)
PMID: 17531483

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: 286 amino acids
Theoretical weight: 33.13 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: O15530 (Residues: 74-359; Coverage: 51%)
Gene names: PDK1, PDPK1
Sequence domains: Protein kinase domain
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SO4 2 x SO4
Ligand 39Z 1 x 39Z
Ligand GOL 3 x GOL
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P3221
Unit cell:
a: 123.951Å b: 123.951Å c: 47.217Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.202 0.2 0.24
Expression system: unidentified baculovirus

Quick links

Citations

4 review citations

Drug discovery approaches targeting the PI3K/Akt pathway in cancer.
Garcia-Echeverria et al. (2008)
3 more

4 mentions without citation

Naproxen induces cell-cycle arrest and apoptosis in human urinary bladder cancer cell lines and chemically induced cancers by targeting PI3K.
Kim et al. (2014)
3 more