6XRN

Crystal structure of human PI3K-gamma in complex with Compound 17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design, Synthesis, and Structure-Activity Relationship Optimization of Pyrazolopyrimidine Amide Inhibitors of Phosphoinositide 3-Kinase gamma (PI3K gamma ).

Mata, G.Miles, D.H.Drew, S.L.Fournier, J.Lawson, K.V.Mailyan, A.K.Sharif, E.U.Yan, X.Beatty, J.W.Banuelos, J.Chen, J.Ginn, E.Chen, A.Gerrick, K.Y.Pham, A.T.Wong, K.Soni, D.Dhanota, P.Shaqfeh, S.G.Meleza, C.Narasappa, N.Singh, H.Zhao, X.Jin, L.Schindler, U.Walters, M.J.Young, S.W.Walker, N.P.Leleti, M.R.Powers, J.P.Jeffrey, J.L.

(2022) J Med Chem 65: 1418-1444

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01153
  • Primary Citation of Related Structures:  
    6XRN

  • PubMed Abstract: 

    Phosphoinositide-3-kinase γ (PI3Kγ) is highly expressed in immune cells and promotes the production and migration of inflammatory mediators. The inhibition of PI3Kγ has been shown to repolarize the tumor immune microenvironment to a more inflammatory phenotype, thereby controlling immune suppression in cancer. Herein, we report the structure-based optimization of an early lead series of pyrazolopyrimidine isoindolinones, which culminated in the discovery of highly potent and isoform-selective PI3Kγ inhibitors with favorable drug-like properties. X-ray cocrystal structure analysis, molecular docking studies, and detailed structure-activity relationship investigations resulted in the identification of the optimal amide and isoindolinone substituents to achieve a desirable combination of potency, selectivity, and metabolic stability. Preliminary in vitro studies indicate that inhibition of PI3Kγ with compound 56 results in a significant immune response by increasing pro-inflammatory cytokine gene expression in M1 macrophages.


  • Organizational Affiliation

    Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform949Homo sapiensMutation(s): 0 
Gene Names: PIK3CG
EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P48736 (Homo sapiens)
Explore P48736 
Go to UniProtKB:  P48736
PHAROS:  P48736
GTEx:  ENSG00000105851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48736
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V84 (Subject of Investigation/LOI)
Query on V84

Download Ideal Coordinates CCD File 
B [auth A]2-amino-5-{2-[(1S)-1-cyclopropylethyl]-7-methyl-1-oxo-2,3-dihydro-1H-isoindol-5-yl}-N-(trans-3-hydroxycyclobutyl)pyrazolo[1,5-a]pyrimidine-3-carboxamide
C25 H28 N6 O3
DKTOKFSQYVFDRK-KKXDTOCCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.205α = 90
b = 68.173β = 95.26
c = 106.8γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references