› 6ez6

X-ray diffraction
2.04Å resolution

PI3 kinase delta in complex with Methyl 5-(4-(5-((4-isopropylpiperazin-1-yl)methyl)oxazol-2-yl)-1H-indazol-6-yl)-2-methoxynicotinate

Released:
DOI: 10.2210/pdb6ez6/pdb
PDB entry 6ez6 coloured by chain, front view.
PDB entry 6ez6 coloured by chain, side view.
PDB entry 6ez6 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Selectively Targeting the Kinome-Conserved Lysine of PI3Kδ as a General Approach to Covalent Kinase Inhibition.
Dalton SE, Dittus L, Thomas DA, Convery MA, Nunes J, Bush JT, Evans JP, Werner T, Bantscheff M, Murphy JA, Campos S
J Am Chem Soc 140 932-939 (2018)
PMID: 29232121

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: 1051 amino acids
Theoretical weight: 120.85 KDa
Source organism: Mus musculus
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O35904 (Residues: 1-105, 106-507, 509-1043; Coverage: 100%)
Gene name: Pik3cd
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand C5Z 1 x C5Z
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: C2
Unit cell:
a: 142.52Å b: 64.35Å c: 116.19Å
α: 90° β: 103.01° γ: 90°
R-values:
R R work R free
0.185 0.183 0.217
Expression system: Spodoptera frugiperda

Quick links

Citations

10 review citations

Kinase inhibitors: the road ahead.
Ferguson et al. (2018)
9 more