8VK6 | pdb_00008vk6

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

• PDB DOI: https://doi.org/10.2210/pdb8VK6/pdb

• Classification: OXIDOREDUCTASE/INHIBITOR
• Organism(s): Saccharomyces cerevisiae YJM789
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2024-01-08 Released: 2025-01-15 
• Deposition Author(s): Tyndall, J.D.A., Monk, B.C., Simons, C.
• Funding Organization(s): European Regional Development Fund, Health Research Council (HRC)

---

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

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

• PubMed: 40403151 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c02922
• Primary Citation 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.
Faculty of Dentistry, Sir John Walsh Research Institute, University of Otago, Dunedin 9016, New Zealand.
School of Pharmacy, University of Otago, Dunedin 9054, New Zealand.
School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, U.K.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.77 kDa 
• Atom Count: 4,532 
• Modeled Residue Count: 527 
• Deposited Residue Count: 539 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lanosterol 14-alpha demethylase	A	539	Saccharomyces cerevisiae YJM789	Mutation(s): 0  Gene Names: ERG11, SCY_2394 EC: 1.14.14.154
UniProt
Find proteins for P10614 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P10614  Go to UniProtKB:  P10614

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
A1AB6 (Subject of Investigation/LOI)	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	E [auth A]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
1PE	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 = 76.686	α = 90
b = 65.537	β = 98.5
c = 80.962	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Tyndall, J.D.A., Monk, B.C., Simons, C.

---

Funding Organization	Location	Grant Number
European Regional Development Fund	European Union	--
Health Research Council (HRC)	New Zealand	19/397

Revision History  

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