› 3h9o

X-ray diffraction
2.3Å resolution

Phosphoinositide-dependent protein kinase 1 (PDK-1) in complex with compound 9

Released:
DOI: 10.2210/pdb3h9o/pdb
PDB entry 3h9o coloured by chain, front view.
PDB entry 3h9o coloured by chain, side view.
PDB entry 3h9o coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Benzo[c][2,7]naphthyridines as inhibitors of PDK-1.
Kim KH, Wissner A, Floyd MB, Fraser HL, Wang YD, Dushin RG, Hu Y, Olland A, Guo B, Arndt K
Bioorg Med Chem Lett 19 5225-8 (2009)
PMID: 19628388

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: 35.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15530 (Residues: 48-359; Coverage: 56%)
Gene names: PDK1, PDPK1
Sequence domains: Protein kinase domain
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 9BD 1 x 9BD
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P3221
Unit cell:
a: 123.77Å b: 123.77Å c: 47.116Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.211 0.209 0.256

Quick links

Citations

1 review citation

The chemical diversity and structure-based discovery of allosteric modulators for the PIF-pocket of protein kinase PDK1.
Xu et al. (2019)
7 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)