6U6A

Crystal structure of Yck2 from Candida albicans in complex with kinase inhibitor GW461484A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Overcoming Fungal Echinocandin Resistance through Inhibition of the Non-essential Stress Kinase Yck2.

Caplan, T.Lorente-Macias, A.Stogios, P.J.Evdokimova, E.Hyde, S.Wellington, M.A.Liston, S.Iyer, K.R.Puumala, E.Shekhar-Guturja, T.Robbins, N.Savchenko, A.Krysan, D.J.Whitesell, L.Zuercher, W.J.Cowen, L.E.

(2020) Cell Chem Biol 27: 269-282.e5

  • DOI: 10.1016/j.chembiol.2019.12.008
  • Primary Citation of Related Structures:  
    6U6A, 6U69

  • PubMed Abstract: 
  • New strategies are urgently needed to counter the threat to human health posed by drug-resistant fungi. To explore an as-yet unexploited target space for antifungals, we screened a library of protein kinase inhibitors for the ability to reverse resis ...

    New strategies are urgently needed to counter the threat to human health posed by drug-resistant fungi. To explore an as-yet unexploited target space for antifungals, we screened a library of protein kinase inhibitors for the ability to reverse resistance of the most common human fungal pathogen, Candida albicans, to caspofungin, a widely used antifungal. This screen identified multiple 2,3-aryl-pyrazolopyridine scaffold compounds capable of restoring caspofungin sensitivity. Using chemical genomic, biochemical, and structural approaches, we established the target for our most potent compound as Yck2, a casein kinase 1 family member. Combination of this compound with caspofungin eradicated drug-resistant C. albicans infection while sparing co-cultured human cells. In mice, genetic depletion of YCK2 caused an ∼3-log 10 decline in fungal burden in a model of systemic caspofungin-resistant C. albicans infection. Structural insights and our tool compound's profile in culture support targeting the Yck2 kinase function as a broadly active antifungal strategy.


    Organizational Affiliation

    Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada. Electronic address: leah.cowen@utoronto.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine protein kinaseA309Candida albicans SC5314Mutation(s): 0 
Gene Names: YCK2orf19.7001CAALFM_C305650WA
Find proteins for A0A1D8PKB4 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Explore A0A1D8PKB4 
Go to UniProtKB:  A0A1D8PKB4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Q0J
Query on Q0J

Download CCD File 
A
2-(4-fluorophenyl)-6-methyl-3-(pyridin-4-yl)pyrazolo[1,5-a]pyridine
C19 H14 F N3
DLJKUEGEDDMTMQ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.563α = 90
b = 91.563β = 90
c = 119.624γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History 

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2020-05-13
    Changes: Database references