3NXU

Crystal structure of human cytochrome P4503A4 bound to an inhibitor ritonavir

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure and mechanism of the complex between cytochrome P4503A4 and ritonavir.

Sevrioukova, I.F., Poulos, T.L.

(2010) Proc Natl Acad Sci U S A 107: 18422-18427

  • DOI: 10.1073/pnas.1010693107
  • Primary Citation of Related Structures:  
    3NXU

  • PubMed Abstract: 

    • Ritonavir is a HIV protease inhibitor routinely prescribed to HIV patients that also potently inactivates cytochrome P4503A4 (CYP3A4), the major human drug-metabolizing enzyme. By inhibiting CYP3A4, ritonavir increases plasma concentrations of other ...

    Ritonavir is a HIV protease inhibitor routinely prescribed to HIV patients that also potently inactivates cytochrome P4503A4 (CYP3A4), the major human drug-metabolizing enzyme. By inhibiting CYP3A4, ritonavir increases plasma concentrations of other anti-HIV drugs oxidized by CYP3A4 thereby improving clinical efficacy. Despite the importance and wide use of ritonavir in anti-HIV therapy, the precise mechanism of CYP3A4 inhibition remains unclear. The available data are inconsistent and suggest that ritonavir acts as a mechanism-based, competitive or mixed competitive-noncompetitive CYP3A4 inactivator. To resolve this controversy and gain functional and structural insights into the mechanism of CYP3A4 inhibition, we investigated the ritonavir binding reaction by kinetic and equilibrium analysis, elucidated how the drug affects redox properties of the hemoprotein, and determined the 2.0 Å X-ray structure of the CYP3A4-ritonavir complex. Our results show that ritonavir is a type II ligand that perfectly fits into the CYP3A4 active site cavity and irreversibly binds to the heme iron via the thiazole nitrogen, which decreases the redox potential of the protein and precludes its reduction with the redox partner, cytochrome P450 reductase.

    Organizational Affiliation: 

    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA. sevrioui@uci.edu



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450 3A4A, B485Homo sapiensMutation(s): 0 
Gene Names: CYP3A3, CYP3A4
EC: 1.14.13.67 (PDB Primary Data), 1.14.13.97 (PDB Primary Data), 1.14.13.32 (PDB Primary Data), 1.14.14.1 (UniProt), 1.14.14.56 (UniProt), 1.14.14.73 (UniProt), 1.14.14.55 (UniProt)
Find proteins for P08684 (Homo sapiens)
Explore P08684 
Go to UniProtKB:  P08684
NIH Common Fund Data Resources
PHAROS  P08684
GTEx  ENSG00000160868
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RIT
Query on RIT
Download CCD File 
A, B
RITONAVIR
C37 H48 N6 O5 S2
NCDNCNXCDXHOMX-XGKFQTDJSA-N		 Ligand Interaction
HEM
Query on HEM
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
DMS
Query on DMS
Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001001 (RIT)
Query on PRD_001001		A, BRITONAVIRPeptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.123α = 90
b = 94.69β = 124.25
c = 93.13γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
CNSrefinement
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other
  • Version 1.3: 2017-11-08
    Changes: Refinement description