7KKE | pdb_00007kke

Phosphoinositide 3-Kinase gamma bound to a thiazole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 
    0.264 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7KKE

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of a Novel Series of Potent and Selective Alkynylthiazole-Derived PI3K gamma Inhibitors.

Bandarage, U.K.Aronov, A.M.Cao, J.Come, J.H.Cottrell, K.M.Davies, R.J.Giroux, S.Jacobs, M.Mahajan, S.Messersmith, D.Moody, C.S.Swett, R.Xu, J.

(2021) ACS Med Chem Lett 12: 129-135

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00573
  • Primary Citation Related Structures: 
    7KKE

  • PubMed Abstract: 

    Phosphoinositide 3-kinases (PI3Ks) are a family of enzymes that control a wide variety of cellular functions such as cell growth, proliferation, differentiation, motility, survival, and intracellular trafficking. PI3Kγ plays a critical role in mediating leukocyte chemotaxis as well as mast cell degranulation, making it a potentially interesting target for autoimmune and inflammatory diseases. We previously disclosed a novel series of PI3Kγ inhibitors derived from a benzothiazole core. The truncation of the benzothiazole core led to the discovery of a structurally diverse alkynyl thiazole series which displayed high PI3Kγ potency and subtype selectivity. Further medicinal chemistry optimization of the alkynyl thiazole series led to identification of compounds such as 14 and 32 , highly potent, subtype selective, and CNS penetrant PI3Kγ inhibitors. Compound 14 showed robust inhibition of PI3Kγ mediated neutrophil migration in vivo .


  • Organizational Affiliation
    • Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States.

Macromolecule Content 

  • Total Structure Weight: 111.66 kDa 
  • Atom Count: 6,825 
  • Modeled Residue Count: 842 
  • Deposited Residue Count: 971 
  • 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 isoform971Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WJV
(Subject of Investigation/LOI)

Query on WJV



Download:Ideal Coordinates CCD File
B [auth A]N-[2-(3,3-dimethylbutoxy)ethyl]-N'-{4-methyl-5-[(pyridin-4-yl)ethynyl]-1,3-thiazol-2-yl}urea
C20 H26 N4 O2 S
LLAXZOBGRHVCCF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
WJV BindingDB:  7KKE Ki: 9 (nM) from 1 assay(s)
IC50: 640 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free:  0.264 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.456α = 90
b = 67.05β = 97.05
c = 107.398γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-AC02-05CH11231

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description