› 4aw0

X-ray diffraction
1.43Å resolution

Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the PIF-Pocket

Released:
DOI: 10.2210/pdb4aw0/pdb
PDB entry 4aw0 coloured by chain, front view.
PDB entry 4aw0 coloured by chain, side view.
PDB entry 4aw0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Substrate-selective inhibition of protein kinase PDK1 by small compounds that bind to the PIF-pocket allosteric docking site.
Busschots K, Lopez-Garcia LA, Lammi C, Stroba A, Zeuzem S, Piiper A, Alzari PM, Neimanis S, Arencibia JM, Engel M, Schulze JO, Biondi RM
Chem Biol 19 1152-63 (2012)
PMID: 22999883

Function and Biology Details

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

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: 311 amino acids
Theoretical weight: 35.47 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O15530 (Residues: 51-359; Coverage: 56%)
Gene names: PDK1, PDPK1
Sequence domains: Protein kinase domain
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand ATP 1 x ATP
Ligand MJF 1 x MJF
Ligand DMS 1 x DMS
Ligand MG 2 x MG
Ligand DTD 1 x DTD
2 modified residues:
Ligand SEP 1 x SEP
Ligand CME 1 x CME

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: C2
Unit cell:
a: 148.27Å b: 44.01Å c: 47.39Å
α: 90° β: 101.57° γ: 90°
R-values:
R R work R free
0.171 0.17 0.188
Expression system: Spodoptera frugiperda

Quick links

Citations

12 review citations

Small-molecule inhibitors of protein-protein interactions: progressing toward the reality.
Arkin et al. (2014)
11 more

5 mentions without citation

The chemical diversity and structure-based discovery of allosteric modulators for the PIF-pocket of protein kinase PDK1.
Xu et al. (2019)
4 more