› 5ngb

X-ray diffraction
2.9Å resolution

X-Ray Diffraction Crystal Structure of the murine PI3K p110delta in complex with a pan inhibitor

Released:
DOI: 10.2210/pdb5ngb/pdb
PDB entry 5ngb coloured by chain, front view.
PDB entry 5ngb coloured by chain, side view.
PDB entry 5ngb coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Identification of a Potent Phosphoinositide 3-Kinase Pan Inhibitor Displaying a Strategic Carboxylic Acid Group and Development of Its Prodrugs.
Pirali T, Ciraolo E, Aprile S, Massarotti A, Berndt A, Griglio A, Serafini M, Mercalli V, Landoni C, Campa CC, Margaria JP, Silva RL, Grosa G, Sorba G, Williams R, Hirsch E, Tron GC
ChemMedChem 12 1542-1554 (2017)
PMID: 28857471

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
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128718 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform Chain: A
Molecule details ›
Chain: A
Length: 1079 amino acids
Theoretical weight: 124.31 KDa
Source organism: Mus musculus
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O35904 (Residues: 1-105, 106-507, 508-1043; Coverage: 100%)
Gene name: Pik3cd
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 8WH 1 x 8WH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: C2221
Unit cell:
a: 63.437Å b: 143.586Å c: 220.193Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.245 0.242 0.29
Expression system: Spodoptera frugiperda

Quick links

Citations

3 review citations

Mechanisms of resistance to estrogen receptor modulators in ER+/HER2- advanced breast cancer.
Zhang et al. (2020)
2 more

2 mentions without citation

Identification of a Potent Phosphoinositide 3-Kinase Pan Inhibitor Displaying a Strategic Carboxylic Acid Group and Development of Its Prodrugs.
Pirali et al. (2017)
1 more