4FIA

Crystal Structure of Human CYP46A1 P450 with bicalutamide Bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

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This is version 1.1 of the entry. See complete history


Literature

Binding of a cyano- and fluoro-containing drug bicalutamide to cytochrome P450 46A1: unusual features and spectral response.

Mast, N.Zheng, W.Stout, C.D.Pikuleva, I.A.

(2013) J Biol Chem 288: 4613-4624

  • DOI: 10.1074/jbc.M112.438754
  • Primary Citation of Related Structures:  
    4FIA

  • PubMed Abstract: 
  • Cytochrome P450 46A1 (CYP46A1) is the cholesterol 24-hydroxylase initiating the major pathways of cholesterol removal from the brain, and bicalutamide (BIC) is a drug of choice for the treatment of progressive androgen-dependent prostate cancer. We evaluated the interactions of BIC with CYP46A1 by x-ray crystallography and by conducting solution and mutagenesis studies ...

    Cytochrome P450 46A1 (CYP46A1) is the cholesterol 24-hydroxylase initiating the major pathways of cholesterol removal from the brain, and bicalutamide (BIC) is a drug of choice for the treatment of progressive androgen-dependent prostate cancer. We evaluated the interactions of BIC with CYP46A1 by x-ray crystallography and by conducting solution and mutagenesis studies. Because BIC is administered to patients as a racemic mixture of the S and R isomers, we studied all three, racemic BIC as well as the S and R isomers. Co-crystallization of CYP46A1 with racemic BIC led to structure determinations at 2.1 Å resolution with the drug complexes exhibiting novel properties. Both BIC isomers bind to the CYP46A1 active site in very similar single orientation and adopt an energetically unfavorable folded conformation. This folded BIC conformation is correlated with drug-induced localized shifts of amino acid side chains in CYP46A1 and unusual interactions in the CYP46A1-BIC complex. One of these interactions involves a water molecule that is coordinated to the P450 heme iron and also hydrogen-bonded to the BIC nitrile. Due to polarization of the water in this environment, the heme elicits previously unreported types of P450 spectral responses. We also observed that access to the P450 active site was affected by differential recognition of S versus R isomers at the CYP46A1 surface arising from BIC conformational polymorphism.


    Organizational Affiliation

    Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cholesterol 24-hydroxylaseA456Homo sapiensMutation(s): 0 
Gene Names: CYP46CYP46A1
EC: 1.14.13.98 (PDB Primary Data), 1.14.14.25 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6A2 (Homo sapiens)
Explore Q9Y6A2 
Go to UniProtKB:  Q9Y6A2
PHAROS:  Q9Y6A2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
198 (Subject of Investigation/LOI)
Query on 198

Download Ideal Coordinates CCD File 
D [auth A]R-BICALUTAMIDE
C18 H14 F4 N2 O4 S
LKJPYSCBVHEWIU-KRWDZBQOSA-N
 Ligand Interaction
0U9 (Subject of Investigation/LOI)
Query on 0U9

Download Ideal Coordinates CCD File 
C [auth A]S-bicalutamide
C18 H14 F4 N2 O4 S
LKJPYSCBVHEWIU-QGZVFWFLSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
198 Binding MOAD:  4FIA Kd: 1800 (nM) from 1 assay(s)
0U9 Binding MOAD:  4FIA Kd: 2900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.053α = 90
b = 121.053β = 90
c = 142.339γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references