6M7X

Structure of human CYP11B1 in complex with fadrozole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.095 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of human cortisol-producing cytochrome P450 11B1 bound to the breast cancer drug fadrozole provides insights for drug design.

Brixius-Anderko, S.Scott, E.E.

(2019) J. Biol. Chem. 294: 453-460

  • DOI: 10.1074/jbc.RA118.006214

  • PubMed Abstract: 
  • Human cytochrome P450 11B1 (CYP11B1) is responsible for the final step generating the steroid hormone cortisol, which controls stress and immune responses and glucose homeostasis. CYP11B1 is a promising drug target to manage Cushing's disease, a diso ...

    Human cytochrome P450 11B1 (CYP11B1) is responsible for the final step generating the steroid hormone cortisol, which controls stress and immune responses and glucose homeostasis. CYP11B1 is a promising drug target to manage Cushing's disease, a disorder arising from excessive cortisol production. However, the design of selective inhibitors has been hampered because structural information for CYP11B1 is unavailable and the enzyme has high amino acid sequence identity (93%) to a closely related enzyme, the aldosterone-producing CYP11B2. Here we report the X-ray crystal structure of human CYP11B1 (at 2.1 Å resolution) in complex with fadrozole, a racemic compound normally used to treat breast cancer by inhibiting estrogen-producing CYP19A1. Comparison of fadrozole-bound CYP11B1 with fadrozole-bound CYP11B2 revealed that despite conservation of the active-site residues, the overall structures and active sites had structural rearrangements consistent with distinct protein functions and inhibition. Whereas fadrozole binds to both CYP11B enzymes by coordinating the heme iron, CYP11B2 binds to the R enantiomer of fadrozole, and CYP11B1 binds to the S enantiomer, each with distinct orientations and interactions. These results provide insights into the cross-reactivity of drugs across multiple steroidogenic cytochrome P450 enzymes, provide a structural basis for understanding human steroidogenesis, and pave the way for the design of more selective inhibitors of each human CYP11B enzyme.


    Organizational Affiliation

    From the Departments of Medicinal Chemistry and.,Pharmacology and the Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109.,From the Departments of Medicinal Chemistry and scottee@umich.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 11B1, mitochondrial
A, B
484Homo sapiensMutation(s): 0 
Gene Names: CYP11B1 (S11BH)
Find proteins for P15538 (Homo sapiens)
Go to Gene View: CYP11B1
Go to UniProtKB:  P15538
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
JD7
Query on JD7

Download SDF File 
Download CCD File 
A, B
4-[(5S)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-5-yl]benzonitrile
fadrozole
C14 H13 N3
CLPFFLWZZBQMAO-AWEZNQCLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JD7Kd: 9 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.095 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.189 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 140.570α = 90.00
b = 140.570β = 90.00
c = 145.777γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-11-28
    Type: Data collection, Database references
  • Version 1.2: 2019-01-23
    Type: Data collection, Database references