5V9L

KRAS G12C in bound to quinazoline based switch II pocket (SWIIP) binder


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.981 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Potent and Selective Covalent Quinazoline Inhibitors of KRAS G12C.

Zeng, M.Lu, J.Li, L.Feru, F.Quan, C.Gero, T.W.Ficarro, S.B.Xiong, Y.Ambrogio, C.Paranal, R.M.Catalano, M.Shao, J.Wong, K.K.Marto, J.A.Fischer, E.S.Janne, P.A.Scott, D.A.Westover, K.D.Gray, N.S.

(2017) Cell Chem Biol 24: 1005-1016.e3

  • DOI: 10.1016/j.chembiol.2017.06.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Targeted covalent small molecules have shown promise for cancers driven by KRAS G12C. Allosteric compounds that access an inducible pocket formed by movement of a dynamic structural element in KRAS, switch II, have been reported, but these compounds ...

    Targeted covalent small molecules have shown promise for cancers driven by KRAS G12C. Allosteric compounds that access an inducible pocket formed by movement of a dynamic structural element in KRAS, switch II, have been reported, but these compounds require further optimization to enable their advancement into clinical development. We demonstrate that covalent quinazoline-based switch II pocket (SIIP) compounds effectively suppress GTP loading of KRAS G12C, MAPK phosphorylation, and the growth of cancer cells harboring G12C. Notably we find that adding an amide substituent to the quinazoline scaffold allows additional interactions with KRAS G12C, and remarkably increases the labeling efficiency, potency, and selectivity of KRAS G12C inhibitors. Structural studies using X-ray crystallography reveal a new conformation of SIIP and key interactions made by substituents located at the quinazoline 2-, 4-, and 7-positions. Optimized lead compounds in the quinazoline series selectively inhibit KRAS G12C-dependent signaling and cancer cell growth at sub-micromolar concentrations.


    Organizational Affiliation

    Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
A, B, C
169Homo sapiensMutation(s): 1 
Gene Names: KRAS (KRAS2, RASK2)
Find proteins for P01116 (Homo sapiens)
Go to Gene View: KRAS
Go to UniProtKB:  P01116
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B, C
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
91D
Query on 91D

Download SDF File 
Download CCD File 
A, B, C
N~3~-[6-chloro-7-(2-fluorophenyl)-4-(4-propanoylpiperazin-1-yl)quinazolin-2-yl]-N,N-dimethyl-beta-alaninamide
C26 H30 Cl F N6 O2
KQSULURPARMUKT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.981 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.171 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 85.062α = 90.00
b = 85.062β = 90.00
c = 130.542γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHASERphasing
HKL-3000data scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-03-23 
  • Released Date: 2017-08-23 
  • Deposition Author(s): Westover, K., Lu, J.

Revision History 

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Database references