6B0Y

Crystal Structure of small molecule ARS-917 covalently bound to K-Ras G12C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The reactivity-driven biochemical mechanism of covalent KRASG12Cinhibitors.

Hansen, R.Peters, U.Babbar, A.Chen, Y.Feng, J.Janes, M.R.Li, L.S.Ren, P.Liu, Y.Zarrinkar, P.P.

(2018) Nat. Struct. Mol. Biol. 25: 454-462

  • DOI: 10.1038/s41594-018-0061-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Activating mutations in KRAS are among the most common tumor driver mutations. Until recently, KRAS had been considered undruggable with small molecules; the discovery of the covalent KRAS <sup>G12C </sup> inhibitors ARS-853 and ARS-1620 has demonstr ...

    Activating mutations in KRAS are among the most common tumor driver mutations. Until recently, KRAS had been considered undruggable with small molecules; the discovery of the covalent KRAS G12C inhibitors ARS-853 and ARS-1620 has demonstrated that it is feasible to inhibit KRAS with high potency in cells and animals. Although the biological activity of these inhibitors has been described, the biochemical mechanism of how the compounds achieve potent inhibition remained incompletely understood. We now show that the activity of ARS-853 and ARS-1620 is primarily driven by KRAS-mediated catalysis of the chemical reaction with Cys12 in human KRAS G12C , while the reversible binding affinity is weak, in the hundreds of micromolar or higher range. The mechanism resolves how an induced, shallow and dynamic pocket not expected to support high-affinity binding of small molecules can nevertheless be targeted with potent inhibitors and may be applicable to other targets conventionally considered undruggable.


    Organizational Affiliation

    Wellspring Biosciences, Inc., San Diego, CA, USA.,Wellspring Biosciences, Inc., San Diego, CA, USA. patrick@wellspringbiosciences.com.,Kura Oncology, Inc., San Diego, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
A, B
170Homo sapiensMutation(s): 4 
Gene Names: KRAS (KRAS2, RASK2)
Find proteins for P01116 (Homo sapiens)
Go to Gene View: KRAS
Go to UniProtKB:  P01116
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
8ZG
Query on 8ZG

Download SDF File 
Download CCD File 
A, B
1-{4-[6-chloro-7-(2-fluorophenyl)quinazolin-4-yl]piperazin-1-yl}propan-1-one
C21 H20 Cl F N4 O
JPFKOCMCIFOGHK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 33.430α = 77.45
b = 39.660β = 81.71
c = 61.850γ = 77.12
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-05-30
    Type: Data collection, Database references
  • Version 1.2: 2018-11-07
    Type: Data collection, Database references