9CD8 | pdb_00009cd8

Crystal Structure of Acetyl-CoA synthetase from Cryptococcus neoformans H99 in complex with inhibitor HGN-1310 (dd3-027)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.219 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Discovery and mechanism of a highly selective, antifungal acetyl-CoA synthetase inhibitor.

Jezewski, A.J.Alden, K.M.Propp, J.Daraji, D.G.Lail 3rd, C.L.Heene, M.E.Fuller, A.J.Ferreira, J.C.Liu, L.Battaile, K.P.Williams, N.S.Staker, B.L.Lovell, S.Hagen, T.J.Krysan, D.J.

(2025) Nat Commun 16: 9118-9118

  • DOI: https://doi.org/10.1038/s41467-025-64183-7
  • Primary Citation of Related Structures:  
    8G0T, 9CD8

  • PubMed Abstract: 

    Acetyl-CoA synthetases (Acs) have emerged as drug targets for the treatment of cancer, metabolic diseases as well as fungal and parasitic infections. Although a variety of small molecule Acs inhibitors have been discovered, the systematic optimization of these molecules has been slowed by a lack of structural information regarding their mechanism of inhibition. Through a chemical genetic-based, synthetic lethal screen of the human fungal pathogen Cryptococcus neoformans, we identified an isoxazole-based Acs inhibitor with antifungal activity and high selectivity for the C. neoformans Acs1 relative to human ACSS2 as well as to other fungal Acs enzymes. Xray crystallography of the isoxazole-CnAcs1 complex revealed that the isoxazole occupies both the acetyl- and CoA-binding sites of CnAcs1. Biochemically, the isoxazoles display uncompetitive inhibition kinetics that are similar to antimalarial Acs inhibitors also proposed to target the CoA binding site. Consequently, these data provide structural and mechanistic insights into the remarkable selectivity of CoA pocket-targeting Acs inhibitors. As such, targeting fungal and parasitic Acs enzymes for the development of novel anti-infectives can be achieved with high selectivity and, thereby, low host toxicity.


  • Organizational Affiliation
    • Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetyl-coenzyme A synthetase694Cryptococcus neoformansMutation(s): 0 
Gene Names: CNAG_00797
EC: 6.2.1.1
UniProt
Find proteins for J9VFT1 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Explore J9VFT1 
Go to UniProtKB:  J9VFT1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ9VFT1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Acetyl-coenzyme A synthetase
B, C
694Cryptococcus neoformansMutation(s): 0 
Gene Names: CNAG_00797
EC: 6.2.1.1
UniProt
Find proteins for J9VFT1 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Explore J9VFT1 
Go to UniProtKB:  J9VFT1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ9VFT1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AV1 (Subject of Investigation/LOI)
Query on A1AV1

Download Ideal Coordinates CCD File 
J [auth A],
P [auth B],
T [auth C]
(5P)-3-azido-N-[(5-cyclopropyl-1,2-oxazol-3-yl)methyl]-5-(2,3-dihydro-1-benzofuran-5-yl)-N-methylbenzamide
C23 H21 N5 O3
QUHPTGKAAIBODP-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
N [auth B],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
K [auth B]
L [auth B]
D [auth A],
E [auth A],
F [auth A],
K [auth B],
L [auth B],
M [auth B],
Q [auth C],
R [auth C],
S [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY
A
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.219 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.224α = 90
b = 176.224β = 90
c = 159.461γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
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 States75N93022C00036
National Institutes of Health/Office of the DirectorUnited StatesS10OD030394

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release