6CR2 | pdb_00006cr2

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 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6CR2

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 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.

Macromolecule Content 

  • Total Structure Weight: 110.74 kDa 
  • Atom Count: 7,762 
  • Modeled Residue Count: 938 
  • Deposited Residue Count: 954 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (PDB Primary Data), 1.14.14.154 (UniProt)
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free:  0.230 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
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

View Full Validation Report



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