9KQS | pdb_00009kqs

Crystal structure of WDR5 in complex with peptide MRTEPRPPAP of EMBOW


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.210 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Therapeutic targeting of WDR5-MLL1 by EMBOW-derived peptides suppresses leukemia progression.

Zhang, M.Chen, M.Li, P.Min, J.

(2025) Cell Chem Biol 

  • DOI: https://doi.org/10.1016/j.chembiol.2025.10.002
  • Primary Citation of Related Structures:  
    9KQS, 9UJR, 9UJZ, 9UK1, 9UK3, 9UK4, 9UK7

  • PubMed Abstract: 

    WD40 repeat-containing protein 5 (WDR5) is a core component of the SET1/mixed lineage leukemia (MLL) complex that regulates gene expression via H3K4 methylation and plays a key role in maintaining oncogenic gene expression programs, particularly in MLL1-rearranged leukemias. In this study, we leveraged a microprotein, endogenous microprotein binder of WDR5 (EMBOW), to develop peptide-based inhibitors that specifically targeted WDR5. Through comprehensive biophysical analyses and high-resolution structural studies, we revealed that EMBOW mainly bound to the WDR5 interaction (WIN) site of WDR5. Structure-guided optimization led to the development of EMBOW-derived peptides, notably Ac7, which exhibited high affinity for WDR5 (K d = 9.17 ± 4.01 nM). These peptides effectively inhibited H3K4 methylation, suppressed oncogenic gene expression, and impeded leukemia cell proliferation in vitro. Importantly, in xenograft mouse models, Ac7 demonstrated significant anti-tumor activity with low toxicity. This work offers a promising strategy for targeting epigenetic regulators with peptide-based therapeutics, providing a foundation for innovative treatments in leukemia.


  • Organizational Affiliation
    • Laboratory of Pesticides and Chemistry Key Laboratory of Ministry of Education, School of Life Sciences, Central China Normal University, Wuhan, Hubei, P.R. China; Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, P.R. China.

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SCRIB overlapping open reading frame proteinA [auth B]10Homo sapiensMutation(s): 0 
UniProt
Find proteins for C0HLS1 (Homo sapiens)
Explore C0HLS1 
Go to UniProtKB:  C0HLS1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC0HLS1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 5B [auth A]313Homo sapiensMutation(s): 0 
Gene Names: WDR5BIG3
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens)
Explore P61964 
Go to UniProtKB:  P61964
PHAROS:  P61964
GTEx:  ENSG00000196363 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61964
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.210 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.56α = 90
b = 81.47β = 90
c = 86.21γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChina--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Database references