6GY0

mPI3Kd IN COMPLEX WITH AZ3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.254 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A class of highly selective inhibitors bind to an active state of PI3K gamma.

Gangadhara, G.Dahl, G.Bohnacker, T.Rae, R.Gunnarsson, J.Blaho, S.Oster, L.Lindmark, H.Karabelas, K.Pemberton, N.Tyrchan, C.Mogemark, M.Wymann, M.P.Williams, R.L.Perry, M.W.D.Papavoine, T.Petersen, J.

(2019) Nat Chem Biol 15: 348-357

  • DOI: 10.1038/s41589-018-0215-0
  • Primary Citation of Related Structures:  
    6GY0

  • PubMed Abstract: 
  • We have discovered a class of PI3Kγ inhibitors exhibiting over 1,000-fold selectivity over PI3Kα and PI3Kβ. On the basis of X-ray crystallography, hydrogen-deuterium exchange-mass spectrometry and surface plasmon resonance experiments we propose that the cyclopropylethyl moiety displaces the DFG motif of the enzyme away from the adenosine tri-phosphate binding site, inducing a large conformational change in both the kinase- and helical domains of PI3Kγ ...

    We have discovered a class of PI3Kγ inhibitors exhibiting over 1,000-fold selectivity over PI3Kα and PI3Kβ. On the basis of X-ray crystallography, hydrogen-deuterium exchange-mass spectrometry and surface plasmon resonance experiments we propose that the cyclopropylethyl moiety displaces the DFG motif of the enzyme away from the adenosine tri-phosphate binding site, inducing a large conformational change in both the kinase- and helical domains of PI3Kγ. Site directed mutagenesis explained how the conformational changes occur. Our results suggest that these cyclopropylethyl substituted compounds selectively inhibit the active state of PI3Kγ, which is unique to these compounds and to the PI3Kγ isoform, explaining their excellent potency and unmatched isoform selectivity that were confirmed in cellular systems. This is the first example of a Class I PI3K inhibitor achieving its selectivity by affecting the DFG motif in a manner that bears similarity to DFG in/out for type II protein kinase inhibitors.


    Organizational Affiliation

    Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden. jens.petersen@astrazeneca.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoformA938Mus musculusMutation(s): 0 
Gene Names: Pik3cd
EC: 2.7.1.153
UniProt
Find proteins for O35904 (Mus musculus)
Explore O35904 
Go to UniProtKB:  O35904
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FGE
Query on FGE

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[4-methyl-5-(1-oxidanylidene-7-sulfamoyl-isoindol-5-yl)-1,3-thiazol-2-yl]ethanamide
C14 H12 N4 O4 S2
LTKQWKJDTSYBED-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.254 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.91α = 90
b = 63.7β = 103.61
c = 115.87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-06-27 
  • Released Date: 2019-02-06 
  • Deposition Author(s): Petersen, J.

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Database references