2V0M

Crystal structure of human P450 3A4 in complex with ketoconazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for Ligand Promiscuity in Cytochrome P450 3A4

Ekroos, M.Sjogren, T.

(2006) Proc.Natl.Acad.Sci.USA 103: 13682

  • DOI: 10.1073/pnas.0603236103
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cytochrome P450 (CYP) 3A4 is the most promiscuous of the human CYP enzymes and contributes to the metabolism of approximately 50% of marketed drugs. It is also the isoform most often involved in unwanted drug-drug interactions. A better understanding ...

    Cytochrome P450 (CYP) 3A4 is the most promiscuous of the human CYP enzymes and contributes to the metabolism of approximately 50% of marketed drugs. It is also the isoform most often involved in unwanted drug-drug interactions. A better understanding of the molecular mechanisms governing CYP3A4-ligand interaction therefore would be of great importance to any drug discovery effort. Here, we present crystal structures of human CYP3A4 in complex with two well characterized drugs: ketoconazole and erythromycin. In contrast to previous reports, the protein undergoes dramatic conformational changes upon ligand binding with an increase in the active site volume by >80%. The structures represent two distinct open conformations of CYP3A4 because ketoconazole and erythromycin induce different types of coordinate shifts. The binding of two molecules of ketoconazole to the CYP3A4 active site and the clear indication of multiple binding modes for erythromycin has implications for the interpretation of the atypical kinetic data often displayed by CYP3A4. The extreme flexibility revealed by the present structures also challenges any attempt to apply computational design tools without the support of relevant experimental data.


    Organizational Affiliation

    AstraZeneca R&D Mölndal, S-431 83 Mölndal, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME P450 3A4
A, B, C, D
485Homo 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
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
KLN
Query on KLN

Download SDF File 
Download CCD File 
A, B, C, D
1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DICHLOROPHENYL)-2-(1H-IMIDAZOL-1-YLMETHYL)-1,3-DIOXOLAN-4-YL]METHOXY}PHENYL)PIPERAZINE
C26 H28 Cl2 N4 O4
XMAYWYJOQHXEEK-ZEQKJWHPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 228.942α = 90.00
b = 66.363β = 102.80
c = 146.419γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-05-15 
  • Released Date: 2007-06-26 
  • Deposition Author(s): Sjogren, T., Ekroos, M.
  • This entry supersedes: 2J0C

Revision History 

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2011-08-03
    Type: Database references, Other, Refinement description, Version format compliance