6Q2T

Human sterol 14a-demethylase (CYP51) in complex with the functionally irreversible inhibitor (R)-N-(1-(3-chloro-4'-fluoro-[1,1'-biphenyl]-4-yl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-(3-fluoro-5-(5-fluoropyrimidin-4-yl)phenyl)-1,3,4-oxadiazol-2-yl)benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Validation of Human Sterol 14 alpha-Demethylase (CYP51) Druggability: Structure-Guided Design, Synthesis, and Evaluation of Stoichiometric, Functionally Irreversible Inhibitors.

Friggeri, L.Hargrove, T.Y.Wawrzak, Z.Guengerich, F.P.Lepesheva, G.I.

(2019) J Med Chem 62: 10391-10401

  • DOI: 10.1021/acs.jmedchem.9b01485
  • Primary Citation of Related Structures:  
    6Q2T

  • PubMed Abstract: 
  • Sterol 14α-demethylases (CYP51) are the cytochrome P450 enzymes required for biosynthesis of sterols in eukaryotes, the major targets for antifungal agents and prospective targets for treatment of protozoan infections. Human CYP51 could be and, for a ...

    Sterol 14α-demethylases (CYP51) are the cytochrome P450 enzymes required for biosynthesis of sterols in eukaryotes, the major targets for antifungal agents and prospective targets for treatment of protozoan infections. Human CYP51 could be and, for a while, was considered as a potential target for cholesterol-lowering drugs (the role that is now played by statins, which are also in clinical trials for cancer) but revealed high intrinsic resistance to inhibition. While microbial CYP51 enzymes are often inhibited stoichiometrically and functionally irreversibly, no strong inhibitors have been identified for human CYP51. In this study, we used comparative structure/functional analysis of CYP51 orthologs from different biological kingdoms and employed site-directed mutagenesis to elucidate the molecular basis for the resistance of the human enzyme to inhibition and also designed, synthesized, and characterized new compounds. Two of them inhibit human CYP51 functionally irreversibly with their potency approaching the potencies of azole drugs currently used to inhibit microbial CYP51.


    Organizational Affiliation

    Vanderbilt-Ingram Cancer Center , Nashville , Tennessee 37232 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lanosterol 14-alpha demethylaseAB446Homo sapiensMutation(s): 0 
Gene Names: CYP51A1CYP51
EC: 1.14.13.70 (PDB Primary Data), 1.14.14.154 (PDB Primary Data)
Find proteins for Q16850 (Homo sapiens)
Explore Q16850 
Go to UniProtKB:  Q16850
NIH Common Fund Data Resources
PHAROS  Q16850
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PJM
Query on PJM

Download CCD File 
A, B
N-[(1R)-1-(3-chloro-4'-fluoro[1,1'-biphenyl]-4-yl)-2-(1H-imidazol-1-yl)ethyl]-4-{5-[3-fluoro-5-(5-fluoropyrimidin-4-yl)phenyl]-1,3,4-oxadiazol-2-yl}benzamide
C36 H23 Cl F3 N7 O2
ZSDQWZVUVIKSDR-YTTGMZPUSA-N
 Ligand Interaction
HEM
Query on HEM

Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
DXC
Query on DXC

Download CCD File 
A
(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
C24 H40 O4
KXGVEGMKQFWNSR-LLQZFEROSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.227 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.664α = 90
b = 117.664β = 90
c = 157.842γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01067871

Revision History 

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence