8EKT | pdb_00008ekt

CYP51 from Acanthamoeba castellanii in complex with the tetrazole-based IND inhibitor VT-1161(VT1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.224 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.213 (Depositor) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Identification of Potent and Selective Inhibitors of Acanthamoeba : Structural Insights into Sterol 14 alpha-Demethylase as a Key Drug Target.

Hargrove, T.Y.Lamb, D.C.Wawrzak, Z.Hull, M.Kelly, S.L.Guengerich, F.P.Lepesheva, G.I.

(2024) J Med Chem 67: 7443-7457

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00303
  • Primary Citation Related Structures: 
    8EKT

  • PubMed Abstract: 

    Acanthamoeba are free-living pathogenic protozoa that cause blinding keratitis, disseminated infection, and granulomatous amebic encephalitis, which is generally fatal. The development of efficient and safe drugs is a critical unmet need. Acanthamoeba sterol 14α-demethylase (CYP51) is an essential enzyme of the sterol biosynthetic pathway. Repurposing antifungal azoles for amoebic infections has been reported, but their inhibitory effects on Acanthamoeba CYP51 enzymatic activity have not been studied. Here, we report catalytic properties, inhibition, and structural characterization of CYP51 from Acanthamoeba castellanii . The enzyme displays a 100-fold substrate preference for obtusifoliol over lanosterol, supporting the plant-like cycloartenol-based pathway in the pathogen. The strongest inhibition was observed with voriconazole (1 h IC 50 0.45 μM), VT1598 (0.25 μM), and VT1161 (0.20 μM). The crystal structures of A. castellanii CYP51 with bound VT1161 (2.24 Å) and without an inhibitor (1.95 Å), presented here, can be used in the development of azole-based scaffolds to achieve optimal amoebicidal effectiveness.


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

Macromolecule Content 

  • Total Structure Weight: 321.55 kDa 
  • Atom Count: 20,818 
  • Modeled Residue Count: 2,478 
  • Deposited Residue Count: 2,760 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
sterol 14a-demethylase
A, B, C, D, E
A, B, C, D, E, F
460Acanthamoeba castellaniiMutation(s): 0 
EC: 1.14.13.70
UniProt
Find proteins for L8GJB3 (Acanthamoeba castellanii (strain ATCC 30010 / Neff))
Explore L8GJB3 
Go to UniProtKB:  L8GJB3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL8GJB3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
VT1
(Subject of Investigation/LOI)

Query on VT1



Download:Ideal Coordinates CCD File
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
(R)-2-(2,4-Difluorophenyl)-1,1-difluoro-3-(1H-tetrazol-1-yl)-1-(5-(4-(2,2,2-trifluoroethoxy)phenyl)pyridin-2-yl)propan-2-ol
C23 H16 F7 N5 O2
IDUYJRXRDSPPRC-NRFANRHFSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.224 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.213 (Depositor) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.453α = 81.22
b = 99.304β = 84.08
c = 107.915γ = 60.08
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data 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 StatesGM067871

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-15
    Changes: Database references
  • Version 1.3: 2026-03-04
    Changes: Refinement description, Structure summary