4I4G

Crystal structure of CYP3A4 ligated to oxazole-substituted desoxyritonavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.718 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Pyridine-Substituted Desoxyritonavir Is a More Potent Inhibitor of Cytochrome P450 3A4 than Ritonavir.

Sevrioukova, I.F.Poulos, T.L.

(2013) J.Med.Chem. 56: 3733-3741

  • DOI: 10.1021/jm400288z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Utilization of the cytochrome P450 3A4 (CYP3A4) inhibitor ritonavir as a pharmacoenhancer for anti-HIV drugs revolutionized the treatment of HIV infection. However, owing to ritonavir-related complications, there is a need for development of new CYP3 ...

    Utilization of the cytochrome P450 3A4 (CYP3A4) inhibitor ritonavir as a pharmacoenhancer for anti-HIV drugs revolutionized the treatment of HIV infection. However, owing to ritonavir-related complications, there is a need for development of new CYP3A4 inhibitors with improved pharmacochemical properties, which requires a full understanding of the CYP3A4 inactivation mechanisms and the unraveling of possible inhibitor binding modes. We investigated the mechanism of CYP3A4 interaction with three desoxyritonavir analogues, containing the heme-ligating imidazole, oxazole, or pyridine group instead of the thiazole moiety (compounds 1, 2, and 3, respectively). Our data show that compound 3 is superior to ritonavir in terms of binding affinity and inhibitory potency owing to greater flexibility and the ability to adopt a conformation that minimizes steric clashing and optimizes protein-ligand interactions. Additionally, Ser119 was identified as a key residue assisting binding of ritonavir-like inhibitors, which emphasizes the importance of polar interactions in the CYP3A4-ligand association.


    Organizational Affiliation

    Departments of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States. sevrioui@uci.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 3A4
A
487Homo sapiensMutation(s): 0 
Gene Names: CYP3A4 (CYP3A3)
EC: 1.14.14.-
Find proteins for P08684 (Homo sapiens)
Go to Gene View: CYP3A4
Go to UniProtKB:  P08684
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Z8Z
Query on Z8Z

Download SDF File 
Download CCD File 
A
N~2~-(methyl{[2-(propan-2-yl)-1,3-thiazol-4-yl]methyl}carbamoyl)-N-[(2R,5R)-5-{[(1,3-oxazol-5-ylmethoxy)carbonyl]amino}-1,6-diphenylhexan-2-yl]-L-valinamide
C37 H48 N6 O5 S
ZBUUPRZMJYAPQF-QSCLJHCWSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Z8ZIC50: 3400 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.718 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.203 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 76.655α = 90.00
b = 99.585β = 90.00
c = 126.375γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Blu-Icedata collection
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-05-01
    Type: Database references
  • Version 1.2: 2013-05-22
    Type: Database references