4D6Z

Cytochrome P450 3A4 bound to imidazole and an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-Based Inhibitor Design for Evaluation of a Cyp3A4 Pharmacophore Model.

Kaur, P.Chamberlin, R.Poulos, T.L.Sevrioukova, I.F.

(2016) J.Med.Chem. 59: 4210

  • DOI: 10.1021/acs.jmedchem.5b01146
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human cytochrome P450 3A4 (CYP3A4) is a key xenobiotic-metabolizing enzyme that oxidizes and clears the majority of drugs. CYP3A4 inhibition may lead to drug-drug interactions, toxicity, and other adverse effects but, in some cases, could be benefici ...

    Human cytochrome P450 3A4 (CYP3A4) is a key xenobiotic-metabolizing enzyme that oxidizes and clears the majority of drugs. CYP3A4 inhibition may lead to drug-drug interactions, toxicity, and other adverse effects but, in some cases, could be beneficial and enhance therapeutic efficiency of coadministered pharmaceuticals that are metabolized by CYP3A4. On the basis of our investigations of analogs of ritonavir, a potent CYP3A4 inactivator and pharmacoenhancer, we have built a pharmacophore model for a CYP3A4-specific inhibitor. This study is the first attempt to test this model using a set of rationally designed compounds. The functional and structural data presented here agree well with the proposed pharmacophore. In particular, we confirmed the importance of a flexible backbone, the H-bond donor/acceptor moiety, and aromaticity of the side group analogous to Phe-2 of ritonavir and demonstrated the leading role of hydrophobic interactions at the sites adjacent to the heme and phenylalanine cluster in the ligand binding process. The X-ray structures of CYP3A4 bound to the rationally designed inhibitors provide deeper insights into the mechanism of the CYP3A4-ligand interaction. Most importantly, two of our compounds (15a and 15b) that are less complex than ritonavir have comparable submicromolar affinity and inhibitory potency for CYP3A4 and, thus, could serve as templates for synthesis of second generation inhibitors for further evaluation and optimization of the pharmacophore model.


    Organizational Affiliation

    Departments of †Pharmaceutical Sciences, ‡Chemistry, and §Molecular Biology and Biochemistry, University of California-Irvine , Irvine, California 92697, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME P450 3A4
A
487Homo sapiensMutation(s): 2 
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PK9
Query on PK9

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Download CCD File 
A
tert-butyl {6-oxo-6-[(pyridin-3-ylmethyl)amino]hexyl}carbamate
C17 H27 N3 O3
LDXDSDSWWMTDPA-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
IMD
Query on IMD

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Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.180 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 77.050α = 90.00
b = 99.400β = 90.00
c = 133.300γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-09-30
    Type: Database references
  • Version 1.2: 2016-05-25
    Type: Database references