2V0M

Crystal structure of human P450 3A4 in complex with ketoconazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 U S A 103: 13682

  • DOI: 10.1073/pnas.0603236103
  • Primary Citation of Related Structures:  
    2V0M, 2J0D

  • 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 of ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME P450 3A4 ABCD485Homo sapiensMutation(s): 0 
Gene Names: CYP3A4CYP3A3
EC: 1.14.14.1 (PDB Primary Data), 1.14.13.67 (PDB Primary Data), 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KLNIC50:  50   nM  BindingDB
KLNIC50:  786   nM  BindingDB
KLNIC50:  60   nM  BindingDB
KKKIC50:  20   nM  BindingDB
KKKIC50:  40   nM  BindingDB
KLNIC50:  280   nM  BindingDB
KKKIC50:  36   nM  BindingDB
KLNIC50:  62   nM  BindingDB
KKKIC50:  15   nM  BindingDB
KLNIC50:  200   nM  BindingDB
KKKIC50:  20   nM  BindingDB
KLNIC50:  140   nM  BindingDB
KLNIC50:  146   nM  BindingDB
KKKIC50:  18   nM  BindingDB
KLNIC50:  2500   nM  BindingDB
KKKIC50:  80000   nM  BindingDB
KKKIC50:  24   nM  BindingDB
KKKIC50:  25   nM  BindingDB
KKKIC50:  22   nM  BindingDB
KKKIC50:  133   nM  BindingDB
KKKIC50:  140   nM  BindingDB
KKKIC50:  150   nM  BindingDB
KLNIC50:  1260   nM  BindingDB
KKKIC50:  12   nM  BindingDB
KKKIC50:  200   nM  BindingDB
KKKIC50:  13   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 228.942α = 90
b = 66.363β = 102.8
c = 146.419γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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
    Changes: Database references, Other, Refinement description, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other