5IS5 | pdb_00005is5

Discovery and Pharmacological Characterization of Novel Quinazoline-based PI3K delta-selective Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb5IS5/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-03-15 Released: 2016-08-10 
• Deposition Author(s): Gutmann, S., Rummel, G., Shrestha, B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.271 (Depositor) 
• R-Value Work: 
  0.229 (Depositor) 

Starting Model: experimental

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

• PubMed: 27563400 
• DOI: https://doi.org/10.1021/acsmedchemlett.6b00119
• Primary Citation 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 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 120.49 kDa 
• Atom Count: 5,917 
• Modeled Residue Count: 785 
• Deposited Residue Count: 1,044 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform	A	1,044	Mus musculus	Mutation(s): 0  Gene Names: Pik3cd EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt)
UniProt
Find proteins for O35904 (Mus musculus) Explore O35904  Go to UniProtKB:  O35904

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6CY	B [auth A]	5-{4-[3-(4-acetylpiperazine-1-carbonyl)phenyl]quinazolin-6-yl}-2-methoxypyridine-3-carbonitrile C28 H24 N6 O3 QYTXJLQBSYAMGR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.271 (Depositor) 
• R-Value Work:  0.229 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.46	α = 90
b = 64.32	β = 103.2
c = 116.64	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Gutmann, S., Rummel, G., Shrestha, B.

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2016-09-14
  Changes: Database references
• Version 1.2: 2017-01-18
  Changes: Data collection
• Version 1.3: 2019-04-24
  Changes: Data collection, Source and taxonomy
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Refinement description