3TJS

Crystal Structure of the complex between human cytochrome P450 3A4 and desthiazolylmethyloxycarbonyl ritonavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Interaction of human cytochrome P4503A4 with ritonavir analogs.

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

(2012) Arch.Biochem.Biophys. 520: 108-116

  • DOI: 10.1016/j.abb.2012.02.018

  • PubMed Abstract: 
  • Ritonavir is a HIV protease inhibitor that also potently inactivates cytochrome P450 3A4 (CYP3A4), a major human drug-metabolizing enzyme. To better understand the mechanism of ligand binding and to find strategies for improvement of the inhibitory p ...

    Ritonavir is a HIV protease inhibitor that also potently inactivates cytochrome P450 3A4 (CYP3A4), a major human drug-metabolizing enzyme. To better understand the mechanism of ligand binding and to find strategies for improvement of the inhibitory potency of ritonavir, currently administered to enhance pharmacokinetics of other anti-HIV drugs that are quickly metabolized by CYP3A4, we compared the manner of CYP3A4 interaction with the drug and two analogs lacking either the heme-ligating thiazole nitrogen or the entire thiazole group. Based on the kinetic, mutagenesis and structural data, we conclude that: (i) the active site residue Arg212 assists binding of all investigated compounds and, thus, may play a more prominent role in metabolic transformation of xenobiotics than previously thought, (ii) peripheral binding of ritonavir limits the heme coordination rate and complicates the binding kinetics, (iii) association of ritonavir-like type II ligands is driven by heme coordination whereas hydrophobic forces define the binding mode, and (iv) substitution of one phenyl group in ritonavir with a smaller hydrophobic moiety could prevent steric clashing and, hence, increase the affinity and inhibitory potency of the drug.


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, Irvine, 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
D0R
Query on D0R

Download SDF File 
Download CCD File 
A
N-[(2S,4S,5S)-5-amino-4-hydroxy-1,6-diphenylhexan-2-yl]-N~2~-(methyl{[2-(propan-2-yl)-1,3-thiazol-4-yl]methyl}carbamoyl)-L-valinamide
desthiazolylmethyloxycarbonyl ritonavir
C32 H45 N5 O3 S
IQKWCORIMSRQGZ-AMEOFWRWSA-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
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001003 (D0R)
Query on PRD_001003
Adesthiazolylmethyloxycarbonyl ritonavirPeptide-like / Antiviral

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.228 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 78.790α = 90.00
b = 98.600β = 90.00
c = 125.070γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
Blu-Icedata collection
PHASERphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-07
    Type: Initial release
  • Version 1.1: 2012-04-04
    Type: Database references
  • Version 1.2: 2012-04-11
    Type: Database references
  • Version 1.3: 2012-12-12
    Type: Other
  • Version 1.4: 2017-06-28
    Type: Database references, Source and taxonomy
  • Version 1.5: 2017-11-08
    Type: Refinement description