KRas G12C in complex with Compound 5c

Experimental Data Snapshot

  • Resolution: 1.79 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Discovery and biological evaluation of 1-{2,7-diazaspiro[3.5]nonan-2-yl}prop-2-en-1-one derivatives as covalent inhibitors of KRAS G12C with favorable metabolic stability and anti-tumor activity.

Imaizumi, T.Akaiwa, M.Abe, T.Nigawara, T.Koike, T.Satake, Y.Watanabe, K.Kaneko, O.Amano, Y.Mori, K.Yamanaka, Y.Nagashima, T.Shimazaki, M.Kuramoto, K.

(2022) Bioorg Med Chem 71: 116949-116949

  • DOI: https://doi.org/10.1016/j.bmc.2022.116949
  • Primary Citation of Related Structures:  
    7YCC, 7YCE

  • PubMed Abstract: 

    RAS protein plays a key role in cellular proliferation and differentiation. RAS gene mutation is a known driver of oncogenic alternation in human cancer. RAS inhibition is an effective therapeutic treatment for solid tumors, but RAS protein has been classified as an undruggable target. Recent reports have demonstrated that a covalent binder to KRAS protein at a mutated cysteine residue (G12C) is effective for the treatment of solid tumors. Here, we report a series of 1-{2,7-diazaspiro[3.5]nonan-2-yl}prop-2-en-1-one derivatives as potent covalent inhibitors against KRAS G12C identified throughout structural optimization of an acryloyl amine moiety to improve in vitro inhibitory activity. From an X-ray complex structural analysis, the 1-{2,7-diazaspiro[3.5]nonan-2-yl}prop-2-en-1-one moiety binds in the switch-II pocket of KRAS G12C. Further optimization of the lead compound (5c) led to the successful identification of 1-[7-[6-chloro-8-fluoro-7-(5-methyl-1H-indazol-4-yl)-2-[(1-methylpiperidin-4-yl)amino]quinazolin-4-yl]-2,7-diazaspiro[3.5]nonan-2-yl]prop-2-en-1-one (7b), a potent compound with high metabolic stabilities in human and mouse liver microsomes. Compound 7b showed a dose-dependent antitumor effect on subcutaneous administration in an NCI-H1373 xenograft mouse model.

  • Organizational Affiliation

    Tsukuba Research Center, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi, Ibaraki 305-8585, Japan. Electronic address: tomoyoshi.imaizumi@astellas.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2B of GTPase KRas
A, B, C
170Homo sapiensMutation(s): 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
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IQC (Subject of Investigation/LOI)
Query on IQC

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C]
C32 H38 Cl F N8 O
Query on GDP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
J [auth C]
C10 H15 N5 O11 P2
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.79 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.268α = 90
b = 94.407β = 91.49
c = 67.423γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2022-08-10 
  • Deposition Author(s): Amano, Y.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description