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

• PDB DOI: https://doi.org/10.2210/pdb9EDX/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Candida albicans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-18 Released: 2025-01-08 
• Deposition Author(s): Stogios, P.J., Whitesell, L., Cowen, L.E., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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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

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

• PubMed: 40038303 
• DOI: https://doi.org/10.1038/s41467-025-57346-z
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada.
Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA.
Department of Biochemistry, University of Texas Southwestern Medical School, Dallas, TX, USA.
Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
Center for Structural Biology of Infectious Diseases (CSBID), Chicago, Illinois, USA.
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.78 kDa 
• Atom Count: 2,572 
• Modeled Residue Count: 306 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
non-specific serine/threonine protein kinase	A	309	Candida albicans	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BIO (Subject of Investigation/LOI)	B [auth A]	2-(4-fluorophenyl)-3-(pyridin-4-yl)pyrazolo[1,5-a]pyridine-6-carbonitrile C19 H11 F N4 LQQPWBQKAOPXPO-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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 = 91.71	α = 90
b = 91.71	β = 90
c = 118.95	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-08 
Deposition Author(s): Stogios, P.J., Whitesell, L., Cowen, L.E., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00035

Revision History  

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