6CR2

Crystal structure of sterol 14-alpha demethylase (CYP51B) from Aspergillus fumigatus in complex with the VNI derivative N-(1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-(2-fluoro-4-(2,2,2-trifluoroethoxy)phenyl)-1,3,4-oxadiazol-2-yl)benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Sterol 14 alpha-Demethylase Structure-Based Design of VNI (( R)- N-(1-(2,4-Dichlorophenyl)-2-(1 H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide)) Derivatives To Target Fungal Infections: Synthesis, Biological Evaluation, and Crystallographic Analysis.

Friggeri, L.Hargrove, T.Y.Wawrzak, Z.Blobaum, A.L.Rachakonda, G.Lindsley, C.W.Villalta, F.Nes, W.D.Botta, M.Guengerich, F.P.Lepesheva, G.I.

(2018) J Med Chem 61: 5679-5691

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00641
  • Primary Citation of Related Structures:  
    6CR2

  • PubMed Abstract: 

    Because of the increase in the number of immunocompromised patients, the incidence of invasive fungal infections is growing, but the treatment efficiency remains unacceptably low. The most potent clinical systemic antifungals (azoles) are the derivatives of two scaffolds: ketoconazole and fluconazole. Being the safest antifungal drugs, they still have shortcomings, mainly because of pharmacokinetics and resistance. Here, we report the successful use of the target fungal enzyme, sterol 14α-demethylase (CYP51), for structure-based design of novel antifungal drug candidates by minor modifications of VNI [( R)- N-(1-(2,4-dichlorophenyl)-2-(1 H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide)], an inhibitor of protozoan CYP51 that cures Chagas disease. The synthesis of fungi-oriented VNI derivatives, analysis of their potencies to inhibit CYP51s from two major fungal pathogens ( Aspergillus fumigatus and Candida albicans), microsomal stability, effects in fungal cells, and structural characterization of A. fumigatus CYP51 in complexes with the most potent compound are described, offering a new antifungal drug scaffold and outlining directions for its further optimization.


  • Organizational Affiliation

    Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
14-alpha sterol demethylase Cyp51B
A, B
477Aspergillus fumigatus Af293Mutation(s): 1 
Gene Names: AFUA_7G03740
EC: 1.14.13.70
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
LFV
Query on LFV

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
N-[(1R)-1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl]-4-{5-[2-fluoro-4-(2,2,2-trifluoroethoxy)phenyl]-1,3,4-oxadiazol-2-yl}benzamide
C28 H19 Cl2 F4 N5 O3
PFDAIZREODDAGQ-DEOSSOPVSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
LFV Binding MOAD:  6CR2 Kd: 20 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.438α = 90
b = 108.438β = 90
c = 90.999γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data 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 General Medical Sciences (NIH/NIGMS)United StatesR01067871

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-07-25
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description