5V9U

Crystal Structure of small molecule ARS-1620 covalently bound to K-Ras G12C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Targeting KRAS Mutant Cancers with a Covalent G12C-Specific Inhibitor.

Janes, M.R.Zhang, J.Li, L.S.Hansen, R.Peters, U.Guo, X.Chen, Y.Babbar, A.Firdaus, S.J.Darjania, L.Feng, J.Chen, J.H.Li, S.Li, S.Long, Y.O.Thach, C.Liu, Y.Zarieh, A.Ely, T.Kucharski, J.M.Kessler, L.V.Wu, T.Yu, K.Wang, Y.Yao, Y.Deng, X.Zarrinkar, P.P.Brehmer, D.Dhanak, D.Lorenzi, M.V.Hu-Lowe, D.Patricelli, M.P.Ren, P.Liu, Y.

(2018) Cell 172: 578-589.e17

  • DOI: 10.1016/j.cell.2018.01.006

  • PubMed Abstract: 
  • KRASG12C was recently identified to be potentially druggable by allele-specific covalent targeting of Cys-12 in vicinity to an inducible allosteric switch II pocket (S-IIP). Success of this approach requires active cycling of KRASG12C between its act ...

    KRASG12C was recently identified to be potentially druggable by allele-specific covalent targeting of Cys-12 in vicinity to an inducible allosteric switch II pocket (S-IIP). Success of this approach requires active cycling of KRASG12C between its active-GTP and inactive-GDP conformations as accessibility of the S-IIP is restricted only to the GDP-bound state. This strategy proved feasible for inhibiting mutant KRAS in vitro; however, it is uncertain whether this approach would translate to in vivo. Here, we describe structure-based design and identification of ARS-1620, a covalent compound with high potency and selectivity for KRASG12C. ARS-1620 achieves rapid and sustained in vivo target occupancy to induce tumor regression. We use ARS-1620 to dissect oncogenic KRAS dependency and demonstrate that monolayer culture formats significantly underestimate KRAS dependency in vivo. This study provides in vivo evidence that mutant KRAS can be selectively targeted and reveals ARS-1620 as representing a new generation of KRASG12C-specific inhibitors with promising therapeutic potential.


    Organizational Affiliation

    Wellspring Biosciences, San Diego, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
A, B
170Homo sapiensMutations: C13G, S52C, L81C, S119C
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

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Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
91S
Query on 91S

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Download CCD File 
A, B
(S)-1-{4-[6-chloro-8-fluoro-7-(2-fluoro-6-hydroxyphenyl)quinazolin-4-yl] piperazin-1-yl}propan-1-one
C21 H19 Cl F2 N4 O2
ICXZXYUITXWHGD-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.149 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 33.440α = 77.48
b = 39.740β = 81.97
c = 61.780γ = 77.20
Software Package:
Software NamePurpose
MOSFLMdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release