5V71

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.228 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

KRAS G12C Drug Development: Discrimination between Switch II Pocket Configurations Using Hydrogen/Deuterium-Exchange Mass Spectrometry.

Lu, J.Harrison, R.A.Li, L.Zeng, M.Gondi, S.Scott, D.Gray, N.S.Engen, J.R.Westover, K.D.

(2017) Structure 25: 1442-1448.e3

  • DOI: 10.1016/j.str.2017.07.003

  • PubMed Abstract: 
  • KRAS G12C, the most common RAS mutation found in non-small-cell lung cancer, has been the subject of multiple recent covalent small-molecule inhibitor campaigns including efforts directed at the guanine nucleotide pocket and separate work focused on ...

    KRAS G12C, the most common RAS mutation found in non-small-cell lung cancer, has been the subject of multiple recent covalent small-molecule inhibitor campaigns including efforts directed at the guanine nucleotide pocket and separate work focused on an inducible pocket adjacent to the switch motifs. Multiple conformations of switch II have been observed, suggesting that switch II pocket (SIIP) binders may be capable of engaging a range of KRAS conformations. Here we report the use of hydrogen/deuterium-exchange mass spectrometry (HDX MS) to discriminate between conformations of switch II induced by two chemical classes of SIIP binders. We investigated the structural basis for differences in HDX MS using X-ray crystallography and discovered a new SIIP configuration in response to binding of a quinazoline chemotype. These results have implications for structure-guided drug design targeting the RAS SIIP.


    Organizational Affiliation

    Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.,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.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA. Electronic address: j.engen@neu.edu.,Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA. Electronic address: kenneth.westover@utsouthwestern.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
A, B, C, D, E, F
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, D, E, F
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
8ZG
Query on 8ZG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
1-{4-[6-chloro-7-(2-fluorophenyl)quinazolin-4-yl]piperazin-1-yl}propan-1-one
C21 H20 Cl F N4 O
JPFKOCMCIFOGHK-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.228 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.169 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 84.933α = 90.00
b = 84.933β = 90.00
c = 130.785γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-3000data scaling
PHENIXrefinement
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-03-17 
  • 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: 2017-09-13
    Type: Database references