6XRL | pdb_00006xrl

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 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6XRL

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 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.

Macromolecule Content 

  • Total Structure Weight: 109.47 kDa 
  • Atom Count: 6,827 
  • Modeled Residue Count: 835 
  • Deposited Residue Count: 949 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
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