3ME6

Crystal structure of cytochrome 2B4 in complex with the anti-platelet drug clopidogrel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of cytochrome P450 2B4 complexed with the antiplatelet drugs ticlopidine and clopidogrel.

Gay, S.C.Roberts, A.G.Maekawa, K.Talakad, J.C.Hong, W.X.Zhang, Q.Stout, C.D.Halpert, J.R.

(2010) Biochemistry 49: 8709-8720

  • DOI: 10.1021/bi100914z
  • Primary Citation of Related Structures:  3KW4
  • Also Cited By: 3R1A, 3R1B, 3TK3, 3UAS

  • PubMed Abstract: 
  • Prior X-ray crystal structures of rabbit cytochrome P450 2B4 (2B4) in complexes with various imidazoles have demonstrated markedly different enzyme conformations depending on the size of the inhibitor occupying the active site. In this study, structu ...

    Prior X-ray crystal structures of rabbit cytochrome P450 2B4 (2B4) in complexes with various imidazoles have demonstrated markedly different enzyme conformations depending on the size of the inhibitor occupying the active site. In this study, structures of 2B4 were determined with the antiplatelet drugs clopidogrel and ticlopidine, which were expected to have greater freedom of movement in the binding pocket. Ticlopidine could be modeled into the electron density maps in two distinct orientations, both of which are consistent with metabolic data gathered with other mammalian P450 enzymes. Results of ligand docking and heme-induced NMR relaxation of drug protons showed that ticlopidine was preferentially oriented with the chlorophenyl group closest to the heme. Because of its stereocenter, clopidogrel was easier to fit in the electron density and exhibited a single orientation, which points the chlorophenyl ring toward the heme. The C(α) traces of both complexes aligned very well with each other and revealed a compact, closed structure that resembles the conformation observed in two previously determined 2B4 structures with the small molecule inhibitors 4-(4-chlorophenyl)imidazole and 1-(4-chlorophenyl)imidazole. The 2B4 active site is able to accommodate small ligands by moving only a small number of side chains, suggesting that ligand reorientation is energetically favored over protein conformational changes for binding of these similarly sized molecules. Adjusting both protein conformation and ligand orientation in the active site gives 2B4 the flexibility to bind to the widest range of molecules, while also being energetically favorable.


    Related Citations: 
    • 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
    • Structural and thermodynamic consequences of 1-(4-chlorophenyl)imidazole binding to cytochrome P450 2B4.
      Zhao, Y.,Sun, L.,Muralidhara, B.K.,White, M.A.,Stout, C.D.,Halpert, J.R.
      (2007) Biochemistry 46: 11559
    • 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
    • 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
    • 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, 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 cuniculusGene 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
CGE
Query on CGE

Download SDF File 
Download CCD File 
A, B, C, D
Clopidogrel
methyl (2S)-(2-chlorophenyl)(6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl)ethanoate
C16 H16 Cl N O2 S
GKTWGGQPFAXNFI-HNNXBMFYSA-N
 Ligand Interaction
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.178 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 234.490α = 90.00
b = 234.490β = 90.00
c = 57.320γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
Blu-Icedata collection
PHASERphasing
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description