7T1H

Crystal structure of CAB1 Pantothenate Kinase from Saccharomyces cerevisiae in complex with compound YU281445


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

High-resolution crystal structure and chemical screening reveal pantothenate kinase as a new target for antifungal development.

Gihaz, S.Gareiss, P.Choi, J.Y.Renard, I.Pal, A.C.Surovsteva, Y.Chiu, J.E.Thekkiniath, J.Plummer, M.Hungerford, W.Montgomery, M.L.Hosford, A.Adams, E.M.Lightfoot, J.D.Fox 3rd, D.Ojo, K.K.Staker, B.L.Fuller, K.Ben Mamoun, C.

(2022) Structure 30: 1494

  • DOI: https://doi.org/10.1016/j.str.2022.09.001
  • Primary Citation of Related Structures:  
    7T1G, 7T1H, 7T1I

  • PubMed Abstract: 

    Fungal infections are the leading cause of mortality by eukaryotic pathogens, with an estimated 150 million severe life-threatening cases and 1.7 million deaths reported annually. The rapid emergence of multidrug-resistant fungal isolates highlights the urgent need for new drugs with new mechanisms of action. In fungi, pantothenate phosphorylation, catalyzed by PanK enzyme, is the first step in the utilization of pantothenic acid and coenzyme A biosynthesis. In all fungi sequenced so far, this enzyme is encoded by a single PanK gene. Here, we report the crystal structure of a fungal PanK alone as well as with high-affinity inhibitors from a single chemotype identified through a high-throughput chemical screen. Structural, biochemical, and functional analyses revealed mechanisms governing substrate and ligand binding, dimerization, and catalysis and helped identify new compounds that inhibit the growth of several Candida species. The data validate PanK as a promising target for antifungal drug development.


  • Organizational Affiliation

    Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pantothenate kinase CAB1
A, B
375Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CAB1YDR531W
EC: 2.7.1.33
UniProt
Find proteins for Q04430 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04430 
Go to UniProtKB:  Q04430
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04430
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E5B (Subject of Investigation/LOI)
Query on E5B

Download Ideal Coordinates CCD File 
C [auth A](8R)-2-{[(4-tert-butylphenyl)methyl]amino}-5-[(morpholin-4-yl)methyl][1,2,4]triazolo[1,5-a]pyrimidin-7(4H)-one
C21 H28 N6 O2
RPOXTKKWAOVEIJ-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.14α = 71.26
b = 52.77β = 85.82
c = 70.57γ = 64.46
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

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 StatesHHSN272201700059C

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2022-10-12
    Changes: Database references
  • Version 1.2: 2022-11-16
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description