7OK4

Crystal Structure of KRasG13C in Complex with Nucleotide-based covalent Inhibitor bdaGDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2B of GTPase KRas170Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VJB (Subject of Investigation/LOI)
Query on VJB

Download Ideal Coordinates CCD File 
B [auth A]bdaGDP
C18 H29 N7 O13 P2
AUZGVMRTRAGZKN-RVXWVPLUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.9α = 90
b = 73.9β = 90
c = 54.8γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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