3LD6

Crystal structure of human lanosterol 14alpha-demethylase (CYP51) in complex with ketoconazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of human CYP51 inhibition by antifungal azoles.

Strushkevich, N.Usanov, S.A.Park, H.W.

(2010) J.Mol.Biol. 397: 1067-1078

  • DOI: 10.1016/j.jmb.2010.01.075

  • PubMed Abstract: 
  • The obligatory step in sterol biosynthesis in eukaryotes is demethylation of sterol precursors at the C14-position, which is catalyzed by CYP51 (sterol 14-alpha demethylase) in three sequential reactions. In mammals, the final product of the pathway ...

    The obligatory step in sterol biosynthesis in eukaryotes is demethylation of sterol precursors at the C14-position, which is catalyzed by CYP51 (sterol 14-alpha demethylase) in three sequential reactions. In mammals, the final product of the pathway is cholesterol, while important intermediates, meiosis-activating sterols, are produced by CYP51. Three crystal structures of human CYP51, ligand-free and complexed with antifungal drugs ketoconazole and econazole, were determined, allowing analysis of the molecular basis for functional conservation within the CYP51 family. Azole binding occurs mostly through hydrophobic interactions with conservative residues of the active site. The substantial conformational changes in the B' helix and F-G loop regions are induced upon ligand binding, consistent with the membrane nature of the protein and its substrate. The access channel is typical for mammalian sterol-metabolizing P450 enzymes, but is different from that observed in Mycobacterium tuberculosis CYP51. Comparison of the azole-bound structures provides insight into the relative binding affinities of human and bacterial P450 enzymes to ketoconazole and fluconazole, which can be useful for the rational design of antifungal compounds and specific modulators of human CYP51.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario, Canada. natstrush@gmail.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lanosterol 14-alpha demethylase
A, B
461Homo sapiensMutation(s): 0 
Gene Names: CYP51A1 (CYP51)
EC: 1.14.14.154
Find proteins for Q16850 (Homo sapiens)
Go to Gene View: CYP51A1
Go to UniProtKB:  Q16850
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KKK
Query on KKK

Download SDF File 
Download CCD File 
A, B
1-acetyl-4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine
C26 H28 Cl2 N4 O4
XMAYWYJOQHXEEK-OZXSUGGESA-N
 Ligand Interaction
BCD
Query on BCD

Download SDF File 
Download CCD File 
A, B
BETA-CYCLODEXTRIN
CYCLO-HEPTA-AMYLOSE
C42 H70 O35
WHGYBXFWUBPSRW-FOUAGVGXSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.212 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 145.726α = 90.00
b = 145.726β = 90.00
c = 110.341γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
CCP4phasing
REFMACrefinement
CCP4model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-01-24
    Type: Structure summary
  • Version 1.3: 2018-04-18
    Type: Data collection