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 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report



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:  
    5IS5, 5ITD

  • 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 sel ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform A1074Homo sapiensMutation(s): 2 
Gene Names: PIK3CA
EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
Find proteins for P42336 (Homo sapiens)
Explore P42336 
Go to UniProtKB:  P42336
NIH Common Fund Data Resources
PHAROS:  P42336
GTEx:  ENSG00000121879
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase regulatory subunit alpha B323Homo sapiensMutation(s): 0 
Gene Names: PIK3R1, GRB1
Find proteins for P27986 (Homo sapiens)
Explore P27986 
Go to UniProtKB:  P27986
NIH Common Fund Data Resources
PHAROS:  P27986
GTEx:  ENSG00000145675
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6CY
Query on 6CY
Download Ideal Coordinates 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:  3440   nM  BindingDB
6CYIC50:  262   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.645α = 90
b = 107.352β = 90
c = 134.502γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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