› 5xgh

X-ray diffraction
2.97Å resolution

Crystal structure of PI3K complex with an inhibitor

Released:
DOI: 10.2210/pdb5xgh/pdb
PDB entry 5xgh coloured by chain, front view.
PDB entry 5xgh coloured by chain, side view.
PDB entry 5xgh coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
New Insights into PI3K Inhibitor Design using X-ray Structures of PI3Kα Complexed with a Potent Lead Compound.
Yang X, Zhang X, Huang M, Song K, Li X, Huang M, Meng L, Zhang J
Sci Rep 7 14572 (2017)
PMID: 29109464

Function and Biology Details

Reactions catalysed: 
ATP + 1-phosphatidyl-1D-myo-inositol = ADP + 1-phosphatidyl-1D-myo-inositol 3-phosphate
ATP + 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate = ADP + 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151133 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform Chain: A
Molecule details ›
Chain: A
Length: 1048 amino acids
Theoretical weight: 122.08 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P42336 (Residues: 8-1055; Coverage: 98%)
Gene name: PIK3CA
Sequence domains:
Phosphatidylinositol 3-kinase regulatory subunit alpha Chain: B
Molecule details ›
Chain: B
Length: 277 amino acids
Theoretical weight: 33.5 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P27986 (Residues: 322-598; Coverage: 38%)
Gene names: GRB1, PIK3R1
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand 84U 1 x 84U
Ligand GOL 1 x GOL
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 70.36Å b: 136.312Å c: 149.408Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.231 0.28
Expression system: Spodoptera frugiperda

Quick links

Citations

3 citation in other articles

SAF-248, a novel PI3Kδ-selective inhibitor, potently suppresses the growth of diffuse large B-cell lymphoma.
Zhang et al. (2022)
2 more

6 mentions without citation

Advances in chemical proteomic evaluation of lipid kinases-DAG kinases as a case study.
Ware et al. (2021)
5 more