› 3qd0

X-ray diffraction
1.99Å resolution

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with (2R,5S)-1-[2-Amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-6-methyl-N-phenyl-3-piperidinecarboxamide

Released:
DOI: 10.2210/pdb3qd0/pdb
PDB entry 3qd0 coloured by chain, front view.
PDB entry 3qd0 coloured by chain, side view.
PDB entry 3qd0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-based design of potent and selective 3-phosphoinositide-dependent kinase-1 (PDK1) inhibitors.
Medina JR, Becker CJ, Blackledge CW, Duquenne C, Feng Y, Grant SW, Heerding D, Li WH, Miller WH, Romeril SP, Scherzer D, Shu A, Bobko MA, Chadderton AR, Dumble M, Gardiner CM, Gilbert S, Liu Q, Rabindran SK, Sudakin V, Xiang H, Brady PG, Campobasso N, Ward P, Axten JM
J Med Chem 54 1871-95 (2011)
PMID: 21341675

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: 312 amino acids
Theoretical weight: 35.65 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O15530 (Residues: 48-359; Coverage: 56%)
Gene names: PDK1, PDPK1
Sequence domains: Protein kinase domain
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand GOL 5 x GOL
Ligand SO4 5 x SO4
Ligand 3Q4 1 x 3Q4
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P3221
Unit cell:
a: 123.943Å b: 123.943Å c: 46.987Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.191 0.189 0.231
Expression system: Spodoptera frugiperda

Quick links

Citations

4 review citations

PI3K signaling in cancer: beyond AKT.
Lien et al. (2017)
3 more

2 mentions without citation

Applying conformational selection theory to improve crossdocking efficiency in 3-phosphoinositide dependent protein kinase-1.
Kotasthane et al. (2014)
1 more