8V5G | pdb_00008v5g

Crystal Structure of Acetyl-CoA synthetase from Cryptococcus neoformans H99 in complex with an ethylsulfamide AMP inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.274 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Synthesis and evaluation of acyl-AMP phosphate isosteres as inhibitors of fungal acetyl CoA synthetase.

Daraji, D.G.Jezewski, A.J.Alden, K.M.Propp, J.P.Heene, M.E.Soldan, C.A.Liu, L.Battaile, K.P.Lovell, S.Staker, B.L.Krysan, D.J.Hagen, T.J.

(2025) Bioorg Med Chem Lett 129: 130389-130389

  • DOI: https://doi.org/10.1016/j.bmcl.2025.130389
  • Primary Citation of Related Structures:  
    5IFI, 8V5G

  • PubMed Abstract: 

    Acetyl-CoA synthetase (ACS) is a member of the adenylate-forming enzymes superfamily. This enzyme plays a crucial role in cellular metabolism. While ACS enzymes are non-essential in mammals, they are essential in some fungal species and parasites that are pathogenic to humans. Hence, inhibition of the ACS enzyme is an emerging target for the development of novel anti-infectives. Alkyl AMP esters and acyl sulfamoyl adenosine (Acyl-AMS) are potent inhibitors of fungal ACS enzymes by mimicingthe acyl-AMP enzyme intermediate. Molecular docking studies were performed to facilitate the design of analogs and to explore their potential ligand-binding interactions with the ACS enzyme. A series of acyl-AMP isosteres were synthesized and screened for inhibitory activity against fungal ACS enzymes. Notably, Compound 14 was successfully crystallized with the Cryptococcus neoformans ACS1 enzyme, providing valuable structural insight for future inhibitor design.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, 60115, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetyl-coenzyme A synthetase
A, B, C
694Cryptococcus neoformansMutation(s): 0 
Gene Names: CNAG_00797
EC: 6.2.1.1
UniProt
Find proteins for J9VFT1 (Cryptococcus neoformans var. grubii serotype A (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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.274 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.01α = 90
b = 183.85β = 93.4
c = 84.725γ = 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: 2023-12-13
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references, Structure summary
  • Version 1.2: 2025-09-17
    Changes: Database references