Crystal Structure of compound 10 covalently bound to K-Ras G12C

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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This is version 1.3 of the entry. See complete history


Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange.

Nnadi, C.I.Jenkins, M.L.Gentile, D.R.Bateman, L.A.Zaidman, D.Balius, T.E.Nomura, D.K.Burke, J.E.Shokat, K.M.London, N.

(2018) J Chem Inf Model 58: 464-471

  • DOI: https://doi.org/10.1021/acs.jcim.7b00399
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The success of targeted covalent inhibitors in the global pharmaceutical industry has led to a resurgence of covalent drug discovery. However, covalent inhibitor design for flexible binding sites remains a difficult task due to a lack of methodological development. Here, we compared covalent docking to empirical electrophile screening against the highly dynamic target K-Ras G12C . While the overall hit rate of both methods was comparable, we were able to rapidly progress a docking hit to a potent irreversible covalent binder that modifies the inactive, GDP-bound state of K-Ras G12C . Hydrogen-deuterium exchange mass spectrometry was used to probe the protein dynamics of compound binding to the switch-II pocket and subsequent destabilization of the nucleotide-binding region. SOS-mediated nucleotide exchange assays showed that, contrary to prior switch-II pocket inhibitors, these new compounds appear to accelerate nucleotide exchange. This study highlights the efficiency of covalent docking as a tool for the discovery of chemically novel hits against challenging targets.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas170Homo sapiensMutation(s): 4 
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
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.28α = 90
b = 94.28β = 90
c = 119.55γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

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 States5R01CA190408-03
Israel Science FoundationIsrael1097/16
National Institutes of Health/National Cancer Institute (NIH/NCI)United States1F30CA214015-01

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description