9NZM | pdb_00009nzm

Crystal Structure of Kirsten Rat Sarcoma G12C Complexed with GMPPNP and Covalently Bound to an Adduct of {(2S)-4-[7-(8-chloronaphthalen-1-yl)-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]-1-[(2Z)-2-fluoro-3-(pyridin-2-yl)prop-2-enoyl]piperazin-2-yl}acetonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 
    0.229 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9NZM

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Covalent inhibitor design confers activity against both GDP- and GTP-bound forms of KRAS G12C.

Condakes, M.L.Zhang, Z.Danahy, D.B.Moore, R.R.Lakkaraju, S.K.Zhuo, X.Amako, Y.Borzilleri, R.M.Balachander, S.B.Chourb, L.Civiello, R.L.Dongre, A.R.Downes, D.P.Drexler, D.M.Dudiak, B.M.Dzhekieva, L.El-Samin, M.Fink, B.E.Frederick, K.Huang, C.Khan, J.Lees, E.Levins, C.G.McCarthy, C.Mintier, G.A.Mosure, K.Parker, M.F.Powles, R.Qi, J.Ruzanov, M.Sharma, S.Sheriff, S.Singh, A.K.Stedman, J.Szapiel, N.Thompson, R.L.Vaccaro, W.Wang, T.Yang, T.You, D.Meyer, M.J.Bronson, J.J.Stewart, M.L.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-69003-0
  • Primary Citation Related Structures: 
    9NZM, 9NZN

  • PubMed Abstract: 

    The discovery of KRAS G12C inactive state inhibitors represented a significant advancement in the field of precision oncology. While inactive state inhibition shows promise in patients, Switch II (SWII)-binding inhibitors targeting both inactive and active states remain an underdeveloped therapeutic modality. Here, we describe the discovery of such KRAS G12C dual inhibitors that bind the SWII allosteric site using a chemically differentiated warhead to covalently modify both the KRAS G12C inactive and active states. Co-crystal structures reveal that these inhibitors perturb a key water-mediated hydrogen bonding network and trigger allosteric remodeling of the GTP-bound protein surface and SWI that prevents binding to downstream effectors. Consistent with simultaneous targeting of the active and inactive states, dual inhibitors provide rapid covalent target engagement and suppression of MAPK signaling. However, they demonstrate similar efficacy in cellular and in vivo models when compared to inactive state-selective ones despite faster target inactivation. Furthermore, both inhibitor classes show similar cellular efficacy in the presence of growth factors that drive KRAS, wt NRAS, and wt HRAS to the active state. These data provide the first detailed account of targeting both the active and inactive states of KRAS G12C and highlight the absence of a mechanistic advantage in contexts dependent on prolonged target inhibition.


  • Organizational Affiliation
    • Bristol Myers Squibb, 250 Water St., Cambridge, MA, USA. matthew@condakes.com.

Macromolecule Content 

  • Total Structure Weight: 41.45 kDa 
  • Atom Count: 2,929 
  • Modeled Residue Count: 321 
  • Deposited Residue Count: 344 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2B of GTPase KRas
A, B
172Homo 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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1B7P
(Subject of Investigation/LOI)

Query on A1B7P



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
{(2S)-4-[7-(8-chloronaphthalen-1-yl)-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]-1-[(3R)-3-fluoro-3-(pyridin-2-yl)propanoyl]piperazin-2-yl}acetonitrile
C37 H40 Cl F N8 O2
CDWZWOHAMHBTAX-WAKHXKBOSA-N
GNP

Query on GNP



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free:  0.229 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.788α = 90
b = 70.42β = 111.07
c = 62.783γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release
  • Version 1.1: 2026-02-11
    Changes: Database references
  • Version 1.2: 2026-03-18
    Changes: Database references