5FRB

Crystal structure of sterol 14-alpha demethylase (CYP51B) from a pathogenic filamentous fungus Aspergillus fumigatus in complex with a tetrazole-based inhibitor VT-1598


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of the New Investigational Drug Candidate VT-1598 in Complex with Aspergillus fumigatus Sterol 14 alpha-Demethylase Provides Insights into Its Broad-Spectrum Antifungal Activity.

Hargrove, T.Y.Garvey, E.P.Hoekstra, W.J.Yates, C.M.Wawrzak, Z.Rachakonda, G.Villalta, F.Lepesheva, G.I.

(2017) Antimicrob Agents Chemother 61

  • DOI: https://doi.org/10.1128/AAC.00570-17
  • Primary Citation of Related Structures:  
    5FRB

  • PubMed Abstract: 

    Within the past few decades, the incidence and complexity of human fungal infections have increased, and therefore, the need for safer and more efficient, broad-spectrum antifungal agents is high. In the study described here, we characterized the new tetrazole-based drug candidate VT-1598 as an inhibitor of sterol 14α-demethylase (CYP51B) from the filamentous fungus Aspergillus fumigatus VT-1598 displayed a high affinity of binding to the enzyme in solution (dissociation constant, 13 ± 1 nM) and in the reconstituted enzymatic reaction was revealed to have an inhibitory potency stronger than the potencies of all other simultaneously tested antifungal drugs, including fluconazole, voriconazole, ketoconazole, and posaconazole. The X-ray structure of the VT-1598/ A. fumigatus CYP51 complex was determined and depicts the distinctive binding mode of the inhibitor in the enzyme active site, suggesting the molecular basis of the improved drug potency and broad-spectrum antifungal activity. These data show the formation of an optimized hydrogen bond between the phenoxymethyl oxygen of VT-1598 and the imidazole ring nitrogen of His374, the CYP51 residue that is highly conserved across fungal pathogens and fungus specific. Comparative structural analysis of A. fumigatus CYP51/voriconazole and Candida albicans CYP51/VT-1161 complexes supports the role of H bonding in fungal CYP51/inhibitor complexes and emphasizes the importance of an optimal distance between this interaction and the inhibitor-heme iron interaction. Cellular experiments using two A. fumigatus strains (strains 32820 and 1022) displayed a direct correlation between the effects of the drugs on CYP51B activity and fungal growth inhibition, indicating the noteworthy anti- A. fumigatus potency of VT-1598 and confirming its promise as a broad-spectrum antifungal agent.


  • Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
STEROL 14-ALPHA DEMETHYLASE, CYP51B473Aspergillus fumigatusMutation(s): 2 
Gene Names: ERG 11
EC: 1.14.13.70 (PDB Primary Data), 1.14.14.154 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for E9QY26 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293))
Explore E9QY26 
Go to UniProtKB:  E9QY26
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9QY26
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
VT2
Query on VT2

Download Ideal Coordinates CCD File 
C [auth A](R)-4-((4-((6-(2-(2,4-difluorophenyl)-1,1-difluoro-2-hydroxy-3-(1H-tetrazol-1-yl)propyl)pyridin-3-yl)ethynyl)phenoxy)methyl)benzonitrile
C31 H22 F4 N6 O2
CHNOUXLXTKTWQU-PMERELPUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.857α = 90
b = 109.857β = 90
c = 84.838γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-05-10
    Changes: Database references
  • Version 1.2: 2017-05-17
    Changes: Database references
  • Version 1.3: 2017-07-05
    Changes: Database references
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description