› 3nun

X-ray diffraction
2.2Å resolution

phosphoinositide-dependent kinase-1 (PDK1) with lead compound

Released:
DOI: 10.2210/pdb3nun/pdb
PDB entry 3nun coloured by chain, front view.
PDB entry 3nun coloured by chain, side view.
PDB entry 3nun coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Aminoindazole PDK1 Inhibitors: A Case Study in Fragment-Based Drug Discovery.
Medina JR, Blackledge CW, Heerding DA, Campobasso N, Ward P, Briand J, Wright L, Axten JM
ACS Med Chem Lett 1 439-42 (2010)
PMID: 24900229

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

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: 292 amino acids
Theoretical weight: 33.79 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: O15530 (Residues: 67-358; Coverage: 53%)
Gene names: PDK1, PDPK1
Sequence domains: Protein kinase domain
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand GOL 4 x GOL
Ligand SO4 6 x SO4
Ligand JMZ 1 x JMZ
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P3221
Unit cell:
a: 122.761Å b: 122.761Å c: 47.106Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.18 0.18 0.227
Expression system: unidentified baculovirus

Quick links

Citations

1 review citation

PDK1 inhibitors.
Barile et al. (2012)
6 other articles

1 mention without citation

Design, Synthesis and Biological Activity Evaluation of S-Substituted 1H-5-Mercapto-1,2,4-Triazole Derivatives as Antiproliferative Agents in Colorectal Cancer.
Mioc et al. (2018)