3KSW

Crystal structure of sterol 14alpha-demethylase (CYP51) from Trypanosoma cruzi in complex with an inhibitor VNF ((4-(4-chlorophenyl)-N-[2-(1H-imidazol-1-yl)-1-phenylethyl]benzamide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural Insights into Inhibition of Sterol 14{alpha}-Demethylase in the Human Pathogen Trypanosoma cruzi.

Lepesheva, G.I.Hargrove, T.Y.Anderson, S.Kleshchenko, Y.Furtak, V.Wawrzak, Z.Villalta, F.Waterman, M.R.

(2010) J Biol Chem 285: 25582-25590

  • DOI: https://doi.org/10.1074/jbc.M110.133215
  • Primary Citation of Related Structures:  
    3K1O, 3KHM, 3KSW

  • PubMed Abstract: 

    Trypanosoma cruzi causes Chagas disease (American trypanosomiasis), which threatens the lives of millions of people and remains incurable in its chronic stage. The antifungal drug posaconazole that blocks sterol biosynthesis in the parasite is the only compound entering clinical trials for the chronic form of this infection. Crystal structures of the drug target enzyme, Trypanosoma cruzi sterol 14alpha-demethylase (CYP51), complexed with posaconazole, another antifungal agent fluconazole and an experimental inhibitor, (R)-4'-chloro-N-(1-(2,4-dichlorophenyl)-2-(1H-imid-azol-1-yl)ethyl)biphenyl-4-carboxamide (VNF), allow prediction of important chemical features that enhance the drug potencies. Combined with comparative analysis of inhibitor binding parameters, influence on the catalytic activity of the trypanosomal enzyme and its human counterpart, and their cellular effects at different stages of the Trypanosoma cruzi life cycle, the structural data provide a molecular background to CYP51 inhibition and azole resistance and enlighten the path for directed design of new, more potent and selective drugs to develop an efficient treatment for Chagas disease.


  • Organizational Affiliation

    Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA. [email protected]


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sterol 14-alpha demethylase458Trypanosoma cruziMutation(s): 2 
Gene Names: CYP51
EC: 1.14.13.70 (PDB Primary Data), 1.14.14.154 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q7Z1V1 (Trypanosoma cruzi (strain CL Brener))
Explore Q7Z1V1 
Go to UniProtKB:  Q7Z1V1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z1V1
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
VNF
Query on VNF

Download Ideal Coordinates CCD File 
C [auth A]4'-chloro-N-[(1R)-2-(1H-imidazol-1-yl)-1-phenylethyl]biphenyl-4-carboxamide
C24 H20 Cl N3 O
CIFIVCCKVZFJFT-QHCPKHFHSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
VNF BindingDB:  3KSW Kd: min: 50, max: 70 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.468α = 90
b = 66.468β = 90
c = 234.281γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description