9BTN | pdb_00009btn

Structure of human SHOC2 in complex with a cyclic peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 
    0.252 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Targeting the SHOC2-RAS interaction in RAS-mutant cancers.

Hauseman, Z.J.Stauffer, F.Beyer, K.S.Molle, S.Cavicchioli, E.Marchand, J.R.Fodor, M.Viscomi, J.Dhembi, A.Katz, S.Faggion, B.Lanter, M.Kerr, G.Schildknecht, D.Handl, C.Maddalo, D.Pissot Soldermann, C.Brady, J.Shrestha, O.Nguyen, Z.Leder, L.Cremosnik, G.Lopez Romero, S.Hassiepen, U.Stams, T.Linder, M.Galli, G.G.Guthy, D.A.King, D.A.Maira, S.M.Thoma, C.R.Ehmke, V.Tordella, L.

(2025) Nature 642: 232-241

  • DOI: https://doi.org/10.1038/s41586-025-08931-1
  • Primary Citation of Related Structures:  
    9BTM, 9BTN, 9BTP, 9OVJ

  • PubMed Abstract: 

    Activating mutations in the rat sarcoma (RAS) genes HRAS, NRAS and KRAS collectively represent the most frequent oncogenic driver in human cancer 1 . They have previously been considered undruggable, but advances in the past few years have led to the clinical development of agents that target KRAS(G12C) and KRAS(G12D) mutants, yielding promises of therapeutic responses at tolerated doses 2 . However, clinical agents that selectively target NRAS(Q61*) mutants (* represents 'any'), the second-most-frequent oncogenic driver in melanoma, are still lacking. Here we identify SHOC2, a component of the SHOC2-MRAS-PP1C complex, as a dependency of RAS(Q61*) tumours in a nucleotide-state-dependent and isoform-agnostic manner. Mechanistically, we found that oncogenic NRAS(Q61R) forms a direct interaction with SHOC2, evidenced by X-ray co-crystal structure. In vitro high-throughput screening enabled the discovery of small molecules that bind to SHOC2 and disrupt the interaction with NRAS(Q61*). Structure-based optimization led to a cellularly active tool compound that shows inhibition of mitogen-activated protein kinase (MAPK) signalling and proliferation in RAS-mutant cancer models, most notably in NRAS(Q61*) settings. These findings provide evidence for a neomorph SHOC2-(canonical)RAS protein interaction that is pharmacologically actionable and relevant to cancer sustenance. Overall, this work provides the concept validation and foundation for developing new therapies at the core of the RAS signalling pathway.


  • Organizational Affiliation

    Novartis BioMedical Research, Cambridge, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich repeat protein SHOC-2505Homo sapiensMutation(s): 0 
Gene Names: SHOC2KIAA0862
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQ13 (Homo sapiens)
Explore Q9UQ13 
Go to UniProtKB:  Q9UQ13
PHAROS:  Q9UQ13
GTEx:  ENSG00000108061 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQ13
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
cyclic peptideB [auth L]15synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth L]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CCS
Query on CCS
B [auth L]L-PEPTIDE LINKINGC5 H9 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free:  0.252 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.764α = 90
b = 69.567β = 90
c = 200.349γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
PHENIXphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release
  • Version 1.1: 2025-05-07
    Changes: Database references
  • Version 1.2: 2025-05-21
    Changes: Database references
  • Version 1.3: 2025-06-18
    Changes: Database references