› 5ack

X-ray diffraction
1.24Å resolution

Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the PIF-Pocket

Released:
DOI: 10.2210/pdb5ack/pdb
PDB entry 5ack coloured by chain, front view.
PDB entry 5ack coloured by chain, side view.
PDB entry 5ack coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of a Potent Allosteric Kinase Modulator by Combining Computational and Synthetic Methods.
Kroon E, Schulze JO, Süß E, Camacho CJ, Biondi RM, Dömling A
Angew Chem Int Ed Engl 54 13933-6 (2015)
PMID: 26385475

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: 35.39 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O15530 (Residues: 50-359; 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 SVQ 1 x SVQ
Ligand DTD 1 x DTD
Ligand DMS 1 x DMS
Ligand NA 3 x NA
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: C2
Unit cell:
a: 147.98Å b: 44.54Å c: 47.81Å
α: 90° β: 101.25° γ: 90°
R-values:
R R work R free
0.143 0.142 0.166
Expression system: Spodoptera frugiperda

Quick links

Citations

3 review citations

Inhibitors of protein-protein interactions (PPIs): an analysis of scaffold choices and buried surface area.
Ran et al. (2018)
2 more

2 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)
1 more