7LXL

Crystal structure of human CYP3A4 bound to the testosterone dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Innovative C 2 -symmetric testosterone and androstenedione dimers: Design, synthesis, biological evaluation on prostate cancer cell lines and binding study to recombinant CYP3A4.

Paquin, A.Oufqir, Y.Sevrioukova, I.F.Reyes-Moreno, C.Berube, G.

(2021) Eur J Med Chem 220: 113496-113496

  • DOI: https://doi.org/10.1016/j.ejmech.2021.113496
  • Primary Citation of Related Structures:  
    7LXL

  • PubMed Abstract: 

    The synthesis of two isomeric testosterone dimers and an androstenedione dimer is reported. The design takes advantage of an efficient transformation of testosterone leading to the synthesis of the key diene, 7α-(buta-1,3-dienyl)-4-androsten-17β-ol-3-one, through an elimination reaction. It was found that in some instances the same reaction led to partial epimerization of the 17β-hydroxyl group into the 17α-hydroxyl group. The specific orientation of the hydroxyl function was confirmed by NMR spectroscopy. Capitalizing on this unforeseen side reaction, several dimers were assembled using an olefin metathesis reaction with Hoveyda-Grubbs catalyst. This led to the formation of two isomeric testosterone dimers with 17α-OH or 17β-OH (14α and 14β) as well as an androstenedione dimer (14). The new dimers and their respective precursors were tested on androgen-dependent (LNCaP) and androgen independent (PC3 and DU145) prostate cancer cells. It was discovered that the most active dimer was made of the natural hormone testosterone (14β) with an average IC 50 of 13.3 μM. In LNCaP cells, 14β was ∼5 times more active than the antiandrogen drug cyproterone acetate (IC 50 of 12.0 μM vs. 59.6 μM, respectively). At low concentrations (0.25-0.5 μM), 14α and 14β were able to completely inhibit LNCaP cell growth induced by testosterone or dihydrotestosterone. Furthermore, cross-reactivity of androgen-based dimers with sterol-metabolizing cytochrome P450 3A4 was explored and the results are disclosed herein.


  • Organizational Affiliation

    Département de Chimie, Biochimie et Physique, Université Du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC, G9A 5H7, Canada; Groupe de Recherche en Signalisation Cellulaire, Université Du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC, G9A 5H7, Canada. Electronic address: Alexis.Paquin@uqtr.ca.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 3A4486Homo sapiensMutation(s): 0 
Gene Names: CYP3A4CYP3A3
EC: 1.14.14.1 (PDB Primary Data), 1.14.14.56 (PDB Primary Data), 1.14.14.73 (PDB Primary Data), 1.14.14.55 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P08684 (Homo sapiens)
Explore P08684 
Go to UniProtKB:  P08684
PHAROS:  P08684
GTEx:  ENSG00000160868 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08684
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YNV (Subject of Investigation/LOI)
Query on YNV

Download Ideal Coordinates CCD File 
C [auth A]17alpha-hydroxy-7alpha-[(2Z)-4-(17beta-hydroxy-3-oxo-8alpha-androst-4-en-7beta-yl)but-2-en-1-yl]-8alpha,10alpha,13alpha,14beta-androst-4-en-3-one
C42 H60 O4
FKJMMUCCAVJSJW-HKNCNPFKSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.869α = 90
b = 101.67β = 90
c = 127.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesES025767

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description