9NZK | pdb_00009nzk

Crystal structure of Yck2 with LY364947


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.211 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

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


Literature

Structure-activity Relationship for Diarylpyrazoles as Inhibitors of the Fungal Kinase Yck2.

Shirley, D.J.Yiu, B.Mancera-Ortiz, I.Stogios, P.J.Liu, Z.Robbins, N.Whitesell, L.Cowen, L.E.Drewry, D.H.Willson, T.M.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.07.12.664496
  • Primary Citation of Related Structures:  
    9NZK

  • PubMed Abstract: 

    Candida albicans is a growing global health threat, causing 1.5 million invasive infections and 1 million deaths annually. Yeast casein kinase 2 (Yck2) in C. albicans has emerged as an antifungal target of the kinase inhibitor LY364947 ( LY ). Herein, we report Yck2 structure-activity relationships for 3,4- and 3,4,5-substituted pyrazole analogs of LY . X-ray crystallography and in vitro profiling revealed the importance of the hinge-binding heterocycle for Yck2 inhibition and fungal kinome selectivity. A hydrogen-bond network between the inhibitor, a bound water molecule, and catalytic residues within the ATP pocket was identified as a key determinant of selectivity over other fungal and human kinases. Phenol analog 11 showed remarkable selectivity for Yck2 and Yck22 over all other C. albicans protein kinases. Several of the LY analogs, including 11 , demonstrated improved antifungal activity. These findings provide a framework for translating human kinase inhibitors into highly selective antifungal Yck2 inhibitors.


  • Organizational Affiliation
    • Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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 A0A8H6C375 (Candida albicans)
Explore A0A8H6C375 
Go to UniProtKB:  A0A8H6C375
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8H6C375
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.211 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.532α = 90
b = 91.532β = 90
c = 118.824γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
PHENIXmodel building
Cootmodel building

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2026-02-25
    Changes: Database references, Other