6XRL

Crystal structure of human PI3K-gamma in complex with inhibitor IPI-549


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of Potent and Selective PI3K gamma Inhibitors.

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

(2020) J Med Chem 63: 11235-11257

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01203
  • Primary Citation of Related Structures:  
    6XRL, 6XRM

  • PubMed Abstract: 

    The selective inhibition of the lipid signaling enzyme PI3Kγ constitutes an opportunity to mediate immunosuppression and inflammation within the tumor microenvironment but is difficult to achieve due to the high sequence homology across the class I PI3K isoforms. Here, we describe the design of a novel series of potent PI3Kγ inhibitors that attain high isoform selectivity through the divergent projection of substituents into both the "selectivity" and "alkyl-induced" pockets within the adenosine triphosphate (ATP) binding site of PI3Kγ. These efforts have culminated in the discovery of 5-[2-amino-3-(1-methyl-1 H -pyrazol-4-yl)pyrazolo[1,5- a ]pyrimidin-5-yl]-2-[(1 S )-1-cyclopropylethyl]-7-(trifluoromethyl)-2,3-dihydro-1 H -isoindol-1-one ( 4 , IC 50 = 0.064 μM, THP-1 cells), which displays >600-fold selectivity for PI3Kγ over the other class I isoforms and is a promising step toward the identification of a clinical development candidate. The structure-activity relationships identified throughout this campaign demonstrate that greater γ-selectivity can be achieved by inhibitors that occupy an "alkyl-induced" pocket and possess bicyclic hinge-binding motifs capable of forming more than one hydrogen bond to the hinge region of PI3Kγ.


  • 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), 2.7.1.137 (UniProt), 2.7.1.154 (UniProt)
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V7Y (Subject of Investigation/LOI)
Query on V7Y

Download Ideal Coordinates CCD File 
B [auth A]2-amino-N-[(1S)-1-{8-[(1-methyl-1H-pyrazol-4-yl)ethynyl]-1-oxo-2-phenyl-1,2-dihydroisoquinolin-3-yl}ethyl]pyrazolo[1,5-a]pyrimidine-3-carboxamide
C30 H24 N8 O2
XUMALORDVCFWKV-IBGZPJMESA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
V7Y BindingDB:  6XRL Kd: 0.29 (nM) from 1 assay(s)
IC50: min: 0.29, max: 2000 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.368α = 90
b = 68.37β = 94.52
c = 107.433γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-10-21
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Advisory, Data collection, Database references