Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.89 kDa 
• Atom Count: 2,621 
• Modelled Residue Count: 306 
• Deposited Residue Count: 309 
• Unique protein chains: 1

 6U6A

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

• PDB DOI: 10.2210/pdb6U6A/pdb

• Classification: TRANSFERASE/TRANSFERASE Inhibitor
• Organism(s): Candida albicans SC5314
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-08-29 Released: 2019-10-30 
• Deposition Author(s): Stogios, P.J., Evdokimova, E., Di Leo, R., Chang, C., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• 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: 2.45 Å
• R-Value Free: 0.212 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

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

• PubMed: 31924499 
• DOI: 10.1016/j.chembiol.2019.12.008
• Primary Citation of Related Structures:  
  6U69, 6U6A


• 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 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.

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Organizational Affiliation: 

Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine protein kinase	A	309	Candida albicans SC5314	Mutation(s): 0  Gene Names: YCK2, orf19.7001, CAALFM_C305650WA
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
Q0J (Subject of Investigation/LOI)	D [auth A]	2-(4-fluorophenyl)-6-methyl-3-(pyridin-4-yl)pyrazolo[1,5-a]pyridine C19 H14 F N3 DLJKUEGEDDMTMQ-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 91.563	α = 90
b = 91.563	β = 90
c = 119.624	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Stogios, P.J., Evdokimova, E., Di Leo, R., Chang, C., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

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