8VK6 | pdb_00008vk6

14alpha-demethylase (CYP51) with amide-linked long arm extension antifungal azole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.226 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Exploring Long Arm Amide-Linked Side Chains in the Design of Antifungal Azole Inhibitors of Sterol 14 alpha-Demethylase (CYP51).

Alsulaimany, M.Keniya, M.V.Alanazi, R.S.N Ruma, Y.Hughes, C.S.Jones, A.T.Tyndall, J.D.A.Parker, J.E.Monk, B.C.Simons, C.

(2025) J Med Chem 68: 10781-10799

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02922
  • Primary Citation of Related Structures:  
    8VK6

  • PubMed Abstract: 

    The rise in fungal drug resistance has exacerbated the treatment of invasive fungal infections, most commonly caused by Candida . This research describes the synthesis of extended "long-arm" azole antifungals that were evaluated against wild-type and resistant fungal species. Biphenyl derivative 22 was the most effective derivative, displaying potent inhibitory activity against Saccharomyces , Candida , and Cryptococcus CYP51 enzymes, including in resistant strains, in comparison with posaconazole. The X-ray crystal structure of S - 22 complexed with S. cerevisiae CYP51 showed a hydrogen bond between the oxygen of the trifluoromethoxy group of S- 22 and the His381 side chain of S. cerevisiae CYP51, which is postulated to contribute significantly to its binding, and stabilization in the presence of the S. cerevisiae CYP51 Y140F/H, C. parapsilosis and C. auris CYP51 Y132F mutations and the C. auris K143R mutation. Computational studies and IC 50 evaluation of compound 22 vs C. albicans wild-type, Y132F, and Y132H/K143 mutant strains supported MIC observations.


  • Organizational Affiliation

    School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lanosterol 14-alpha demethylase539Saccharomyces cerevisiae YJM789Mutation(s): 0 
Gene Names: ERG11SCY_2394
EC: 1.14.14.154
UniProt
Find proteins for P10614 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P10614 
Go to UniProtKB:  P10614
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10614
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 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
A1AB6 (Subject of Investigation/LOI)
Query on A1AB6

Download Ideal Coordinates CCD File 
C [auth A]N-[(2S)-2-(2,4-difluorophenyl)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]-4'-(trifluoromethoxy)[1,1'-biphenyl]-4-carboxamide
C25 H19 F5 N4 O3
QMPFWCWUYMNPNU-DEOSSOPVSA-N
LMT
Query on LMT

Download Ideal Coordinates CCD File 
E [auth A]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
D [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.226 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.686α = 90
b = 65.537β = 98.5
c = 80.962γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Regional Development FundEuropean Union--
Health Research Council (HRC)New Zealand19/397

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2025-07-30
    Changes: Database references