9QXZ | pdb_00009qxz

Structure of human NONO bound to (R)-SKBG-1 in p212121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.253 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structural basis for NONO-specific modification by the alpha-chloroacetamide compound (R)-SKBG-1.

Florio, A.V.Bure, C.Fribourg, S.

(2026) Cell Chem Biol 33: 268-275.e3

  • DOI: https://doi.org/10.1016/j.chembiol.2025.12.013
  • Primary Citation Related Structures: 
    9QXZ, 9QZL

  • PubMed Abstract: 

    Among the many proteins involved in cancer progression, an increasing number of RNA-binding proteins (RBPs) are central to the function of a cell and tightly associated to genetic diseases. In a recent study, small-molecule inhibitors have been identified as targeting NONO, an RBP known to be involved in mRNA splicing, DNA repair, and membraneless organelle stability. Here, we report the molecular basis of NONO targeting by the α-chloroacetamide molecule (R)-SKBG-1, its specific binding to NONO, and the enantiomer selectivity on the basis of mass spectrometry measurements and structure determination. We have determined the crystal structure of (R)-SKBG-1-bound to NONO homodimer. This study sheds light on the conformational plasticity of (R)-SKBG-1 when covalently bound to NONO. Altogether, these results give an experimental rationale for ligand modification and optimization in a future use as a drug against cancer.


  • Organizational Affiliation
    • INSERM U1212, CNRS UMR5320, Université de Bordeaux, 2 Rue Hoffmann Martinot, 33000 Bordeaux, France; Department of Biological, Chemical and Pharmaceutical Sciences and Technology, University of Palermo, Via Archirafi 28, Palermo, Italy.

Macromolecule Content 

  • Total Structure Weight: 179.03 kDa 
  • Atom Count: 12,233 
  • Modeled Residue Count: 1,475 
  • Deposited Residue Count: 1,536 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Non-POU domain-containing octamer-binding protein
A, B, C, D, E
A, B, C, D, E, F
256Homo sapiensMutation(s): 0 
Gene Names: NONONRB54
UniProt & NIH Common Fund Data Resources
Find proteins for Q15233 (Homo sapiens)
Explore Q15233 
Go to UniProtKB:  Q15233
PHAROS:  Q15233
GTEx:  ENSG00000147140 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15233
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JB9
(Subject of Investigation/LOI)

Query on A1JB9



Download:Ideal Coordinates CCD File
G [auth A],
H [auth D]
4-(2-chloranylethanoyl)-~{N}-[(4-methoxyphenyl)methyl]-1-(4-methoxyphenyl)sulfonyl-piperazine-2-carboxamide
C22 H26 Cl N3 O6 S
SXQZEMXQTRNLRZ-HXUWFJFHSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.253 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.258α = 90
b = 127.098β = 90
c = 201.445γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-12-17 
  • Deposition Author(s): Fribourg, S.

Funding OrganizationLocationGrant Number
Institut National de la Sante et de la Recherche Medicale (INSERM)France--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2026-07-01
    Changes: Database references, Structure summary