7RTQ

Sterol 14alpha demethylase (CYP51) from Naegleria fowleri in complex with an inhibitor R)-N-(1-(3,4'-difluorobiphenyl-4-yl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Relaxed Substrate Requirements of Sterol 14 alpha-Demethylase from Naegleria fowleri Are Accompanied by Resistance to Inhibition.

Hargrove, T.Y.Wawrzak, Z.Rachakonda, G.Nes, W.D.Villalta, F.Guengerich, F.P.Lepesheva, G.I.

(2021) J Med Chem 64: 17511-17522

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01710
  • Primary Citation of Related Structures:  
    7RTQ

  • PubMed Abstract: 

    Naegleria fowleri is the protozoan pathogen that causes primary amoebic meningoencephalitis (PAM), with the death rate exceeding 97%. The amoeba makes sterols and can be targeted by sterol biosynthesis inhibitors. Here, we characterized N. fowleri sterol 14-demethylase, including catalytic properties and inhibition by clinical antifungal drugs and experimental substituted azoles with favorable pharmacokinetics and low toxicity. None of them inhibited the enzyme stoichiometrically. The highest potencies were displayed by posaconazole (IC 50 = 0.69 μM) and two of our compounds (IC 50 = 1.3 and 0.35 μM). Because both these compounds penetrate the brain with concentrations reaching minimal inhibitory concentration (MIC) values in an N. fowleri cellular assay, we report them as potential drug candidates for PAM. The 2.1 Å crystal structure, in complex with the strongest inhibitor, provides an explanation connecting the enzyme weaker substrate specificity with lower sensitivity to inhibition. It also provides insight into the enzyme/ligand molecular recognition process and suggests directions for the design of more potent inhibitors.


  • 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
Protein CYP51
A, B, C, D
466Naegleria fowleriMutation(s): 0 
Gene Names: NF0102700
UniProt
Find proteins for A0A2H4A2U9 (Naegleria fowleri)
Explore A0A2H4A2U9 
Go to UniProtKB:  A0A2H4A2U9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2H4A2U9
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 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
7PW (Subject of Investigation/LOI)
Query on 7PW

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
N-[(1R)-2-(1H-imidazol-1-yl)-1-(3,4',5-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide
C32 H22 F3 N5 O2
VZHXYQRJRDRVFA-NDEPHWFRSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.062α = 89.49
b = 75.223β = 74.63
c = 105.953γ = 63.98
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

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 StatesGM067871

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2022-01-19
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description