9PIZ | pdb_00009piz

Structure of KRAS-G12C bound to 1-[(4aR,10P,13R)-10-[5-amino-4-fluoro-3-methyl-2-(trifluoromethyl)phenyl]-11-chloro-9-fluoro-1,2,4a,5-tetrahydropyrazino[1',2':4,5][1,4]oxazino[2,3-c]quinolin-3(4H)-yl]prop-2-en-1-one (compound 15)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 
    0.218 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery and Optimization of a Potent, Efficacious, and Brain-Penetrant Inhibitor of KRAS G12C.

Landry, M.L.Malhotra, S.Beresini, M.Chan, C.Chan, E.de la Cruz, C.C.Endres, N.F.Evangelista, M.Gustafson, A.Hu, D.Hunsaker, T.Hsu, P.Izrayelit, Y.La, H.Saenz-Lopez Larrocha, P.Lian, Q.Merchant, M.Mao, J.Mroue, R.Oh, A.Plise, E.Shao, C.Siu, M.Tran, J.C.Wang, Y.Wang, W.Wei, B.Wong, S.Yen, C.W.Zhou, Y.Purkey, H.E.Heffron, T.P.Salphati, L.

(2026) J Med Chem 69: 5241-5258

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02279
  • Primary Citation Related Structures: 
    9PIZ

  • PubMed Abstract: 

    Mutant KRAS is highly prevalent in human cancer and has been actively pursued as a target for drug discovery. Much progress has been made in drugging KRAS G12C, owing to the ability of inhibitors to covalently target its oncogenic cysteine mutation at codon 12. A number of KRAS G12C inhibitors have advanced to clinical development and are being investigated for the treatment of a variety of solid tumors. Notably, many patients with KRAS G12C-positive non-small cell lung cancer develop brain metastases. Herein, we report the discovery and development of a brain-penetrant inhibitor of KRAS G12C using divarasib as a starting point. Optimization efforts focused on reducing molecular weight and topological polar surface area as well as shielding of hydrogen bond donors. In this manner, active transport by both P-gp and breast cancer resistance protein (BCRP) was attenuated, and high exposure in rodent brain tissue was achieved.


  • Organizational Affiliation
    • Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States.

Macromolecule Content 

  • Total Structure Weight: 68.37 kDa 
  • Atom Count: 4,910 
  • Modeled Residue Count: 603 
  • Deposited Residue Count: 612 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2B of GTPase KRas171Homo sapiensMutation(s): 1 
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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-KRAS heavy chainB [auth H]226synthetic constructMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-KRAS light chainC [auth I]215synthetic constructMutation(s): 0 

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CII
(Subject of Investigation/LOI)

Query on A1CII



Download:Ideal Coordinates CCD File
F [auth A]1-[(4aR,10P,13R)-10-[5-amino-4-fluoro-3-methyl-2-(trifluoromethyl)phenyl]-11-chloro-9-fluoro-1,2,4a,5-tetrahydropyrazino[1',2':4,5][1,4]oxazino[2,3-c]quinolin-3(4H)-yl]prop-2-en-1-one
C25 H20 Cl F5 N4 O2
DNDDKPAWCOTOAU-GFCCVEGCSA-N
GDP

Query on GDP



Download:Ideal Coordinates CCD File
E [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
G [auth H]
J [auth H]
L [auth H]
N [auth I]
O [auth I]
G [auth H],
J [auth H],
L [auth H],
N [auth I],
O [auth I],
Q [auth I],
S [auth I]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
I [auth H],
M [auth H],
P [auth I]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
K [auth H],
R [auth I]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.767α = 90
b = 69β = 114.19
c = 100.987γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-11
    Type: Initial release
  • Version 1.1: 2026-03-25
    Changes: Database references