9XZ1 | pdb_00009xz1

KRAS(G12C)-RNK07311-HSP90(N-terminus)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.249 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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Literature

Chaperone directed heterobifunctional molecules circumvent KRAS G12C inhibitor resistance.

Pulido, I.Luan, Q.Pastor-Puente, S.Gunder, L.Wang, Y.Ying, C.Li, J.Sun, Y.Dai, Y.Ascoli, C.Abdelhady, K.Massad, M.Prince, T.L.Wang, G.Foley, K.P.Ying, W.Papautsky, I.Carretero, J.Shimamura, T.

(2025) Cancer Lett 622: 217691-217691

  • DOI: https://doi.org/10.1016/j.canlet.2025.217691
  • Primary Citation of Related Structures:  
    9XZ1

  • PubMed Abstract: 

    While KRAS G12C inhibitors have shown promising results in clinical activity, acquired resistance remains a significant barrier to durable responses. Combination therapies have been explored to improve the efficacy of KRAS G12C inhibitors; however, their use is often restricted due to toxicity and limitations in clinically amenable dosing schedules. Transcriptomic profiling and functional assays on acquired resistant models to adagrasib identified an enrichment of HSP90 client proteins in resistant phenotypes, suggesting a therapeutic vulnerability. To address the finding, RNK07421, a novel heterobifunctional molecule, was developed to simultaneously target KRAS G12C and HSP90-client oncoproteins. Structural and biochemical analyses demonstrated that RNK07421 disrupts KRAS G12C interactions by inducing a non-natural interface with HSP90, thereby impairing oncogenic signaling. In vitro, RNK07421 effectively suppressed ERK reactivation and reduced viability in KRAS G12C -mutant cell lines exhibiting either intrinsic or acquired resistance. In vivo, RNK07421 significantly reduced tumor burden in xenograft models, outperforming both monotherapies and combination therapies. These findings highlight dual KRAS G12C and HSP90 inhibition as a promising strategy to overcome resistance in KRAS G12C -driven cancers.


  • Organizational Affiliation
    • Department of Surgery, Division of Cardiothoracic Surgery, University of Illinois Chicago, Chicago, IL, 60612, USA; University of Illinois Hospital & Health Sciences System Cancer Center, University of Illinois Chicago, Chicago, IL, 60612, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alpha236Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1HSP90AHSPC1HSPCA
EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens)
Explore P07900 
Go to UniProtKB:  P07900
PHAROS:  P07900
GTEx:  ENSG00000080824 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07900
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas170Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CRY (Subject of Investigation/LOI)
Query on A1CRY

Download Ideal Coordinates CCD File 
F [auth B](5M)-4-{4-[(4-{4-[2-({7-(8-chloronaphthalen-1-yl)-4-[(3S)-3-(cyanomethyl)-4-propanoylpiperazin-1-yl]-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-2-yl}oxy)ethyl]piperazine-1-carbonyl}piperidin-1-yl)methyl]phenyl}-5-[2,4-dihydroxy-5-(propan-2-yl)phenyl]-4H-1,2,4-triazole-3-carboxamide
C57 H66 Cl N13 O6
NDQUNBVBLOTAMF-RWYGWLOXSA-N
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
E [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
BTB
Query on BTB

Download Ideal Coordinates CCD File 
C [auth A]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.249 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.575α = 90
b = 42.537β = 110.58
c = 95.283γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
Cootmodel building

Structure Validation

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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: 2025-10-15
    Type: Initial release