3G93

Single ligand occupancy crystal structure of cytochrome P450 2B4 in complex with the inhibitor 1-biphenyl-4-methyl-1H-imidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of cytochrome P450 2B4 in complex with the inhibitor 1-biphenyl-4-methyl-1H-imidazole: ligand-induced structural response through alpha-helical repositioning.

Gay, S.C.Sun, L.Maekawa, K.Halpert, J.R.Stout, C.D.

(2009) Biochemistry 48: 4762-4771

  • DOI: 10.1021/bi9003765
  • Primary Citation of Related Structures:  
  • Also Cited By: 3UAS, 3TK3, 3R1B, 3R1A, 3ME6, 3KW4

  • PubMed Abstract: 
  • Two different ligand occupancy structures of cytochrome P450 2B4 (CYP2B4) in complex with 1-biphenyl-4-methyl-1H-imidazole (1-PBI) have been determined by X-ray crystallography. 1-PBI belongs to a series of tight binding, imidazole-based CYP2B4 inhib ...

    Two different ligand occupancy structures of cytochrome P450 2B4 (CYP2B4) in complex with 1-biphenyl-4-methyl-1H-imidazole (1-PBI) have been determined by X-ray crystallography. 1-PBI belongs to a series of tight binding, imidazole-based CYP2B4 inhibitors. 1-PBI binding to CYP2B4 yields a type II spectrum with a K(s) value of 0.23 microM and inhibits enzyme activity with an IC(50) value of 0.035 microM. Previous CYP2B4 structures have shown a large degree of structural movement in response to ligand size. With two phenyl rings, 1-PBI is larger than 1-(4-chlorophenyl)imidazole (1-CPI) and 4-(4-chlorophenyl)imidazole (4-CPI) but smaller than bifonazole, which is branched and contains three phenyl rings. The CYP2B4-1-PBI complex is a structural intermediate to the closed CPI and the open bifonazole structures. The B/C-loop reorganizes itself to include two short partial helices while closing one side of the active site. The F-G-helix cassette pivots over the I-helix in direct response to the size of the ligand in the active site. A cluster of Phe residues at the fulcrum of this pivot point allows for dramatic repositioning of the cassette with only a relatively small amount of secondary structure rearrangement. Comparisons of ligand-bound CYP2B4 structures reveal trends in plastic region mobility that could allow for predictions of their position in future structures based on ligand shape and size.


    Related Citations: 
    • Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9 {angstrom} resolution: Insight into the range of P450 conformations and coordination of redox partner binding.
      Scott, E.E.,White, M.A.,He, Y.A.,Johnson, E.F.,Stout, C.D.,Halpert, J.R.
      (2004) J.Biol.Chem. 279: 27294
    • Structural and thermodynamic consequences of 1-(4-chlorophenyl)imidazole binding to cytochrome P450 2B4.
      Zhao, Y.,Sun, L.,Muralidhara, B.K.,Kumar, S.,White, M.A.,Stout, C.D.,Halpert, J.R.
      (2007) Biochemistry 46: 11559
    • An open conformation of mammalian cytochrome P450 2B4 at 1.6 A resolution.
      Scott, E.E.,He, Y.A.,Wester, M.R.,White, M.A.,Chin, C.C.,Halpert, J.R.,Johnson, E.F.,Stout, C.D.
      (2003) Proc.Natl.Acad.Sci.USA 100: 13196
    • Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction.
      Zhao, Y.,White, M.A.,Muralidhara, B.K.,Sun, L.,Halpert, J.R.,Stout, C.D.
      (2006) J.Biol.Chem. 281: 5973


    Organizational Affiliation

    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093, USA. scgay@ucsd.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 2B4
A, B, C, D
476Oryctolagus cuniculusMutation(s): 9 
Gene Names: CYP2B4
EC: 1.14.14.1
Find proteins for P00178 (Oryctolagus cuniculus)
Go to UniProtKB:  P00178
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
PB2
Query on PB2

Download SDF File 
Download CCD File 
A, C, D
1-(biphenyl-4-ylmethyl)-1H-imidazole
C16 H14 N2
DLYMRVCQTVOYEW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.910α = 90.00
b = 151.815β = 90.00
c = 181.583γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASESphasing
MOSFLMdata reduction
SCALAdata scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance