› 2pe2

X-ray diffraction
2.13Å resolution

CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) 3-{5-[2-Oxo-5-ureido-1,2-dihydro-indol-(3Z)-ylidenemethyl]-1H-pyrrol-3-yl}-N-(2-piperidin-1-yl-ethyl)-benzamide COMPLEX

Released:
DOI: 10.2210/pdb2pe2/pdb
PDB entry 2pe2 coloured by chain, front view.
PDB entry 2pe2 coloured by chain, side view.
PDB entry 2pe2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors. Part 2: optimization of BX-517.
Islam I, Brown G, Bryant J, Hrvatin P, Kochanny MJ, Phillips GB, Yuan S, Adler M, Whitlow M, Lentz D, Polokoff MA, Wu J, Shen J, Walters J, Ho E, Subramanyam B, Zhu D, Feldman RI, Arnaiz DO
Bioorg Med Chem Lett 17 3819-25 (2007)
PMID: 17544272

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

Assemblies composition:
monomeric (preferred)
homo dimer
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 3 x SO4
Ligand 464 1 x 464
Ligand GOL 8 x GOL
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: 123.223Å b: 123.223Å c: 47.386Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.189 0.188 0.215
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

3 mentions without citation

Using a Genetically Encoded Sensor to Identify Inhibitors of Toxoplasma gondii Ca2+ Signaling.
Sidik et al. (2016)
2 more