9YGS | pdb_00009ygs

Crystal structure of GMPPNP bound KRAS-Y71H in complex with RBD domain of CRAF(RAF1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 
    0.233 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Disrupted molecular glue complex drives RAS inhibitor resistance.

Sang, B.Ye, L.F.Fu, Z.Pourfarjam, Y.Cuevas-Navarro, A.Fan, S.Hu, F.Washington, A.Rodriguez, D.J.Vides, A.Kar, S.Ahler, E.Lin, K.K.Hegde, A.Smith, J.A.M.Wolpin, B.M.Punekar, S.R.Spira, A.I.Garrido-Laguna, I.Hong, D.S.Dar, A.C.Yaeger, R.Arbour, K.C.Lito, P.

(2026) Cell 

  • DOI: https://doi.org/10.1016/j.cell.2026.03.031
  • Primary Citation Related Structures: 
    9YGS, 9YOW

  • PubMed Abstract: 

    Tri-complex inhibitors (TCIs) are molecular glues that bind the active, guanosine triphosphate (GTP)-bound state of RAS and recruit cyclophilin A (CYPA) to form a synthetic complex that blocks oncogenic signaling. Although these agents have shown clinical activity in RAS mutant cancers, resistance mechanisms remain poorly defined. Here, we analyzed paired baseline and end-of-treatment samples from 40 patients treated with the RAS inhibitor daraxonrasib and identified recurrent alterations in 18 cases. Structural and functional analyses revealed that acquired mutations confer resistance by disrupting interactions essential for daraxonrasib binding to RAS, including RAS Y64 mutations, or by enhancing the RAS-RAF interaction, thereby favoring native RAS-RAF signaling, including RAS Y71 or kinase-dead/hypoactive BRAF mutations. We then identified a TCI that targets RAS Y64 mutants and combination therapies to target resistance driven by kinase-dead BRAF. These findings uncover convergent resistance mechanisms that undermine the molecular glue function and offer a mechanistic blueprint for enhancing therapeutic efficacy in RAS-driven malignancies.


  • Organizational Affiliation
    • Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Macromolecule Content 

  • Total Structure Weight: 29.1 kDa 
  • Atom Count: 2,127 
  • Modeled Residue Count: 245 
  • Deposited Residue Count: 251 
  • Unique protein chains: 2

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)
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116-2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
RAF proto-oncogene serine/threonine-protein kinase80Homo sapiensMutation(s): 0 
Gene Names: RAF1RAF
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04049 (Homo sapiens)
Go to UniProtKB:  P04049
PHAROS:  P04049
GTEx:  ENSG00000132155 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04049-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.265α = 90
b = 71.236β = 90
c = 44.896γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-20
    Type: Initial release