8CX5

Crystal Structure of small molecule alpha,beta-ketoamide 4 covalently bound to K-Ras(G12R)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Chemoselective Covalent Modification of K-Ras(G12R) with a Small Molecule Electrophile.

Zhang, Z.Morstein, J.Ecker, A.K.Guiley, K.Z.Shokat, K.M.

(2022) J Am Chem Soc 144: 15916-15921

  • DOI: https://doi.org/10.1021/jacs.2c05377
  • Primary Citation of Related Structures:  
    8CX5

  • PubMed Abstract: 

    KRAS mutations are one of the most common oncogenic drivers in human cancer. While small molecule inhibitors for the G12C mutant have been successfully developed, allele-specific inhibition for other KRAS hotspot mutants remains challenging. Here we report the discovery of covalent chemical ligands for the common oncogenic mutant K-Ras(G12R). These ligands bind in the Switch II pocket and irreversibly react with the mutant arginine residue. An X-ray crystal structure reveals an imidazolium condensation product formed between the α,β-diketoamide ligand and the ε- and η-nitrogens of arginine 12. Our results show that arginine residues can be selectively targeted with small molecule electrophiles despite their weak nucleophilicity and provide the basis for the development of mutant-specific therapies for K-Ras(G12R)-driven cancer.


  • Organizational Affiliation

    Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California 94158, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2B of GTPase KRas
A, B
170Homo sapiensMutation(s): 4 
Gene Names: KRASKRAS2RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P7U (Subject of Investigation/LOI)
Query on P7U

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
{(2S)-4-[(7P)-7-(8-chloronaphthalen-1-yl)-8-fluoro-2-{[(4R,7as)-tetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-4-yl]-1-[(3S)-2,2,3-trihydroxybutanoyl]piperazin-2-yl}acetonitrile
C35 H37 Cl F N7 O5
ODVFPOIDMRCQHU-GMAHTHKFSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
K [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.21α = 90
b = 65.661β = 101.85
c = 61.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States1R01CA244550

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-31
    Type: Initial release
  • Version 1.1: 2022-09-07
    Changes: Database references
  • Version 1.2: 2022-09-14
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary