5ITD

Crystal structure of PI3K alpha with PI3K delta inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Discovery and Pharmacological Characterization of Novel Quinazoline-Based PI3K Delta-Selective Inhibitors.

Hoegenauer, K., Soldermann, N., Stauffer, F., Furet, P., Graveleau, N., Smith, A.B., Hebach, C., Hollingworth, G.J., Lewis, I., Gutmann, S., Rummel, G., Knapp, M., Wolf, R.M., Blanz, J., Feifel, R., Burkhart, C., Zecri, F.

(2016) Acs Med.Chem.Lett. 7: 762-767

  • DOI: 10.1021/acsmedchemlett.6b00119
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Inhibition of the lipid kinase PI3Kδ is a promising principle to treat B and T cell driven inflammatory diseases. Using a scaffold deconstruction-reconstruction strategy, we identified 4-aryl quinazolines that were optimized into potent PI3Kδ isoform ...

    Inhibition of the lipid kinase PI3Kδ is a promising principle to treat B and T cell driven inflammatory diseases. Using a scaffold deconstruction-reconstruction strategy, we identified 4-aryl quinazolines that were optimized into potent PI3Kδ isoform selective analogues with good pharmacokinetic properties. With compound 11, we illustrate that biochemical PI3Kδ inhibition translates into modulation of isoform-dependent immune cell function (human, rat, and mouse). After oral administration of compound 11 to rats, proximal PD markers are inhibited, and dose-dependent efficacy in a mechanistic plaque forming cell assay could be demonstrated.

    Organizational Affiliation: 

    Global Discovery Chemistry, Center for Proteomic Chemistry, Metabolism and Pharmacokinetics, Autoimmunity, Transplantation and Inflammation, Novartis Institutes for BioMedical Research , Novartis Campus, CH-4002 Basel, Switzerland.,Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 5300 Chiron Way, Emeryville, California 94608, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
A
1074Homo sapiensMutation(s): 2 
Gene Names: PIK3CA
EC: 2.7.1.153
Find proteins for P42336 (Homo sapiens)
Go to Gene View: PIK3CA
Go to UniProtKB:  P42336
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 3-kinase regulatory subunit alpha
B
323Homo sapiensMutation(s): 0 
Gene Names: PIK3R1 (GRB1)
Find proteins for P27986 (Homo sapiens)
Go to Gene View: PIK3R1
Go to UniProtKB:  P27986
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6CY
Query on 6CY
Download SDF File 
Download CCD File 
A
5-{4-[3-(4-acetylpiperazine-1-carbonyl)phenyl]quinazolin-6-yl}-2-methoxypyridine-3-carbonitrile
C28 H24 N6 O3
QYTXJLQBSYAMGR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6CYIC50: 262 - 3440 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 104.645α = 90.00
b = 107.352β = 90.00
c = 134.502γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-07
    Type: Initial release