9EDX | pdb_00009edx

Crystal structure of Yck2 from Candida albicans in complex with inhibitor 2a: 2-(4-fluorophenyl)-3-(pyridin-4-yl)pyrazolo[1,5-a]pyridine-6-carbonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.239 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structure-guided optimization of small molecules targeting Yck2 as a strategy to combat Candida albicans.

Puumala, E.Nandakumar, M.Yiu, B.Stogios, P.J.Strickland, B.G.Zarnowski, R.Wang, X.Williams, N.S.Savchenko, A.Andes, D.R.Robbins, N.Whitesell, L.Willson, T.M.Cowen, L.E.

(2025) Nat Commun 16: 2156-2156

  • DOI: https://doi.org/10.1038/s41467-025-57346-z
  • Primary Citation of Related Structures:  
    9EDV, 9EDW, 9EDX, 9EDY

  • PubMed Abstract: 

    Candida albicans is the most common cause of life-threatening fungal infection in the developed world but remains a therapeutic challenge. Protein kinases have been rewarding drug targets across diverse indications but remain untapped for antifungal development. Previously, screening kinase inhibitors against C. albicans revealed a 2,3-aryl-pyrazolopyridine, GW461484A (GW), which targets casein kinase 1 (CK1) family member Yck2. Here, we report optimization of GW via two complementary approaches, synthesis of bioisosteres possessing an imidazo[1,2-a]pyridine core, and R-group substitution of GW's pyrazolo[1,5-a]pyridine core. Characterization of compounds reveals two 6-cyano derivatives with improved pharmacological properties that retain whole-cell bioactivity and selectivity for fungal Yck2 compared to human CK1α. Efficacy studies in mice indicate both analogs possess single-agent activity against C. albicans resistant to first-line echinocandin antifungals and potentiate non-curative echinocandin treatment. Results validate Yck2 as an antifungal target and encourage further development of inhibitors acting by this previously unexploited mode of action.


  • Organizational Affiliation
    • Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
non-specific serine/threonine protein kinase309Candida albicansMutation(s): 0 
Gene Names: FOB64_000203
EC: 2.7.11.1
UniProt
Find proteins for A0A1D8PKB4 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Explore A0A1D8PKB4 
Go to UniProtKB:  A0A1D8PKB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D8PKB4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.239 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.71α = 90
b = 91.71β = 90
c = 118.95γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93022C00035

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-08
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Database references