6P8Y

Crystal structure of human KRAS G12C covalently bound to an acryloylazetidine acetamide inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery ofN-(1-Acryloylazetidin-3-yl)-2-(1H-indol-1-yl)acetamides as Covalent Inhibitors of KRASG12C.

Shin, Y.Jeong, J.W.Wurz, R.P.Achanta, P.Arvedson, T.Bartberger, M.D.Campuzano, I.D.G.Fucini, R.Hansen, S.K.Ingersoll, J.Iwig, J.S.Lipford, J.R.Ma, V.Kopecky, D.J.McCarter, J.San Miguel, T.Mohr, C.Sabet, S.Saiki, A.Y.Sawayama, A.Sethofer, S.Tegley, C.M.Volak, L.P.Yang, K.Lanman, B.A.Erlanson, D.A.Cee, V.J.

(2019) Acs Med.Chem.Lett. 10: 1302-1308

  • DOI: 10.1021/acsmedchemlett.9b00258
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • KRAS regulates many cellular processes including proliferation, survival, and differentiation. Point mutants of KRAS have long been known to be molecular drivers of cancer. <i>KRAS p.G12C </i>, which occurs in approximately 14% of lung adenocarcinom ...

    KRAS regulates many cellular processes including proliferation, survival, and differentiation. Point mutants of KRAS have long been known to be molecular drivers of cancer. KRAS p.G12C , which occurs in approximately 14% of lung adenocarcinomas, 3-5% of colorectal cancers, and low levels in other solid tumors, represents an attractive therapeutic target for covalent inhibitors. Herein, we disclose the discovery of a class of novel, potent, and selective covalent inhibitors of KRAS G12C identified through a custom library synthesis and screening platform called Chemotype Evolution and structure-based design. Identification of a hidden surface groove bordered by H95/Y96/Q99 side chains was key to the optimization of this class of molecules. Best-in-series exemplars exhibit a rapid covalent reaction with cysteine 12 of GDP-KRAS G12C with submicromolar inhibition of downstream signaling in a KRAS G12C -specific manner.


    Organizational Affiliation

    Departments of Therapeutic Discovery, Oncology Research, Pharmacokinetics and Drug Metabolism, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States.,Carmot Therapeutics, Inc. 740 Heinz Avenue, Berkeley, California 94710, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
A, B
183Homo sapiensMutation(s): 3 
Gene Names: KRAS (KRAS2, RASK2)
Find proteins for P01116 (Homo sapiens)
Go to Gene View: KRAS
Go to UniProtKB:  P01116
Small Molecules
Ligands 3 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
O5Y
Query on O5Y

Download SDF File 
Download CCD File 
A, B
2-[5-bromo-3-(5-methoxy-3,4-dihydroisoquinoline-2(1H)-carbonyl)-1H-indol-1-yl]-N-(1-propanoylazetidin-3-yl)acetamide
C27 H29 Br N4 O4
ZVWBSEHSMCJHSP-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 33.756α = 90.00
b = 106.045β = 93.90
c = 39.900γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MxDCdata collection
HKL-2000data reduction
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
Cootmodel building
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-06-08 
  • Released Date: 2019-08-28 
  • Deposition Author(s): Mohr, C.

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-10-02
    Type: Data collection, Database references