Crystal Structure of KRasG13C in Complex with Nucleotide-based Covalent Inhibitor edaGDP

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

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Targeting oncogenic KRasG13C with nucleotide-based covalent inhibitors.

Goebel, L.Kirschner, T.Koska, S.Rai, A.Janning, P.Maffini, S.Vatheuer, H.Czodrowski, P.Goody, R.S.Muller, M.P.Rauh, D.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.82184
  • Primary Citation of Related Structures:  
    7OK3, 7OK4

  • PubMed Abstract: 

    Mutations within Ras proteins represent major drivers in human cancer. In this study, we report the structure-based design, synthesis, as well as biochemical and cellular evaluation of nucleotide-based covalent inhibitors for KRasG13C, an important oncogenic mutant of Ras that has not been successfully addressed in the past. Mass spectrometry experiments and kinetic studies reveal promising molecular properties of these covalent inhibitors, and X-ray crystallographic analysis has yielded the first reported crystal structures of KRasG13C covalently locked with these GDP analogues. Importantly, KRasG13C covalently modified with these inhibitors can no longer undergo SOS-catalysed nucleotide exchange. As a final proof-of-concept, we show that in contrast to KRasG13C, the covalently locked protein is unable to induce oncogenic signalling in cells, further highlighting the possibility of using nucleotide-based inhibitors with covalent warheads in KRasG13C-driven cancer.

  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2B of 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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VJ8 (Subject of Investigation/LOI)
Query on VJ8

Download Ideal Coordinates CCD File 
B [auth A]edaGDP
C16 H25 N7 O13 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.4α = 90
b = 73.4β = 90
c = 54.2γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyRA 1055/5-1
German Research Foundation (DFG)GermanyGO 284/10-1

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references
  • Version 1.2: 2023-04-05
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description