9NCW | pdb_00009ncw

Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.275 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.249 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 
    0.251 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Development and characterization of triazole-based WDR5 inhibitors for the treatment of glioblastoma.

Coker, J.A.Martinez, S.R.Han, S.H.Sloan, A.R.Gupta, A.K.Bukenya, G.Polzer, P.Ramos, J.H.Rico, E.G.Rico, A.Lindsey, A.A.Navadgi, T.Reitz, N.Romigh, T.Macdonald, J.Sonawane, D.Goins, C.M.Hubert, C.G.Wang, N.S.Cheng, F.Alvarado, J.Sprowls, S.A.Lathia, J.D.Stauffer, S.R.

(2026) JCI Insight 

  • DOI: https://doi.org/10.1172/jci.insight.198298
  • Primary Citation Related Structures: 
    9NCT, 9NCV, 9NCW

  • PubMed Abstract: 

    Glioblastoma (GBM) cancer stem cells (CSCs) contribute to tumor recurrence, treatment resistance, and dismal clinical outcomes. Genetic and pharmacological evidence suggests that the nuclear scaffolding protein WD-repeat containing protein 5 (WDR5) is a therapeutic vulnerability of the CSC population. However, previously reported WDR5 inhibitors display low permeability and are unable to penetrate the blood-brain barrier (BBB), limiting their utility in GBM. Herein, we report the structure-guided development of a novel series of triazole-based WDR5 WIN-site inhibitors designed to increase passive brain penetration. We identified triazole-based WDR5 inhibitors that are potent, passively permeable, and in some cases more brain penetrant than other scaffolds. We phenotypically assessed our novel WDR5 inhibitors in a panel of patient-derived CSC models and uncovered unique WDR5-regulated metabolic genes in GBM. We also evaluated their antiproliferative activity against CSCs both in vitro and in vivo. Finally, to identify novel combination opportunities, we screened a 2,100-compound chemical probe library and identified that the ATAD2 inhibitor BAY-850 synergizes with WDR5 inhibitors to enhance CSC killing. Our work diversifies the chemical matter targeting WDR5, clarifies the in vitro consequences of WIN-site inhibition in CSCs, and encourages the future development of next-generation WDR5 inhibitors with the potential to achieve in vivo efficacy in the brain.


  • Organizational Affiliation
    • Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, United States of America.

Macromolecule Content 

  • Total Structure Weight: 189.37 kDa 
  • Atom Count: 10,305 
  • Modeled Residue Count: 1,184 
  • Deposited Residue Count: 1,696 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
WD repeat-containing protein 5
A, B, C, D
424Homo 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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BW9
(Subject of Investigation/LOI)

Query on A1BW9



Download:Ideal Coordinates CCD File
E [auth A],
F [auth B]
1-{[(6P)-3-[(3,5-dimethoxyphenyl)methyl]-6-(4-fluoro-2-methylphenyl)-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazol-8-yl]methyl}-3-methyl-1,3-dihydro-2H-imidazol-2-imine
C31 H31 F N6 O2
CMPQOOWMXHVBSV-QOSDPKFLSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.275 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.249 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 0.251 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.534α = 91.293
b = 68.696β = 103.26
c = 93.018γ = 90.383
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

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: 2025-08-13
    Type: Initial release
  • Version 1.1: 2026-05-20
    Changes: Database references