4H6O

Sterol 14-alpha demethylase (CYP51)from Trypanosoma cruzi in complex with the inhibitor NEU321 (1-(3-(4-chloro-3,5-dimethylphenoxy)benzyl)-1H-imidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.264 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Antitrypanosomal Lead Discovery: Identification of a Ligand-Efficient Inhibitor of Trypanosoma cruzi CYP51 and Parasite Growth.

Andriani, G.Amata, E.Beatty, J.Clements, Z.Coffey, B.J.Courtemanche, G.Devine, W.Erath, J.Juda, C.E.Wawrzak, Z.Wood, J.T.Lepesheva, G.I.Rodriguez, A.Pollastri, M.P.

(2013) J Med Chem 56: 2556-2567

  • DOI: https://doi.org/10.1021/jm400012e
  • Primary Citation of Related Structures:  
    4H6O

  • PubMed Abstract: 

    Chagas disease is caused by the intracellular protozoan parasite Trypanosomal cruzi , and current drugs are lacking in terms of desired safety and efficacy profiles. Following on a recently reported high-throughput screening campaign, we have explored initial structure-activity relationships around a class of imidazole-based compounds. This profiling has uncovered compounds 4c (NEU321) and 4j (NEU704), which are potent against in vitro cultures of T. cruzi and are greater than 160-fold selective over host cells. We report in vitro drug metabolism and properties profiling of 4c and show that this chemotype inhibits the T. cruzi CYP51 enzyme, an observation confirmed by X-ray crystallographic analysis. We compare the binding orientation of 4c to that of other, previously reported inhibitors. We show that 4c displays a significantly better ligand efficiency and a shorter synthetic route over previously disclosed CYP51 inhibitors, and should therefore be considered a promising lead compound for further optimization.


  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sterol 14-alpha demethylase461Trypanosoma cruziMutation(s): 3 
Gene Names: CYP51
EC: 1.14.13.70
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
NEE
Query on NEE

Download Ideal Coordinates CCD File 
C [auth A]1-[3-(4-chloro-3,5-dimethylphenoxy)benzyl]-1H-imidazole
C18 H17 Cl N2 O
KRDUMXYLMIWMMP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.264 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.29α = 90
b = 63.29β = 90
c = 223.995γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-03-27
    Changes: Database references
  • Version 1.2: 2013-04-10
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description