5AJR

Sterol 14-alpha demethylase (CYP51) from Trypanosoma cruzi in complex with the 1-tetrazole derivative VT-1161 ((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)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Clinical Candidate Vt-1161'S Antiparasitic Effect in Vitro, Activity in a Murine Model of Chagas Disease, and Structural Characterization in Complex with the Target Enzyme Cyp51 from Trypanosoma Cruzi.

Hoekstra, W.J.Hargrove, T.Y.Wawrzak, Z.Da Gama Jaen Batista, D.Da Silva, C.F.Nefertiti, A.S.G.Rachakonda, G.Schotzinger, R.J.Villalta, F.Soeiro, M.D.N.C.Lepesheva, G.I.

(2015) Antimicrob Agents Chemother 60: 1058

  • DOI: https://doi.org/10.1128/AAC.02287-15
  • Primary Citation of Related Structures:  
    5AJR

  • PubMed Abstract: 

    A novel antifungal drug candidate, the 1-tetrazole-based agent VT-1161 [(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], which is currently in two phase 2b antifungal clinical trials, was found to be a tight-binding ligand (apparent dissociation constant [Kd], 24 nM) and a potent inhibitor of cytochrome P450 sterol 14α-demethylase (CYP51) from the protozoan pathogen Trypanosoma cruzi. Moreover, VT-1161 revealed a high level of antiparasitic activity against amastigotes of the Tulahuen strain of T. cruzi in cellular experiments (50% effective concentration, 2.5 nM) and was active in vivo, causing >99.8% suppression of peak parasitemia in a mouse model of infection with the naturally drug-resistant Y strain of the parasite. The data strongly support the potential utility of VT-1161 in the treatment of Chagas disease. The structural characterization of T. cruzi CYP51 in complex with VT-1161 provides insights into the molecular basis for the compound's inhibitory potency and paves the way for the further rational development of this novel, tetrazole-based inhibitory chemotype both for antiprotozoan chemotherapy and for antifungal chemotherapy.


  • Organizational Affiliation

    Viamet Pharmaceuticals, Inc., Durham, North Carolina, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
STEROL 14-ALPHA DEMETHYLASE460Trypanosoma cruziMutation(s): 0 
EC: 1.14.13.70 (PDB Primary Data), 1.14.14.154 (UniProt)
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
VT1
Query on VT1

Download Ideal Coordinates CCD File 
C [auth A](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: 2.75 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.06α = 90
b = 63.06β = 90
c = 221.75γ = 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 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-02
    Type: Initial release
  • Version 1.1: 2015-12-23
    Changes: Database references, Structure summary
  • Version 1.2: 2016-02-10
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description