4H1N

Crystal Structure of P450 2B4 F297A Mutant in Complex with Anti-platelet Drug Clopidogrel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray crystal structure of the cytochrome P450 2B4 active site mutant F297A in complex with clopidogrel: Insights into compensatory rearrangements of the binding pocket.

Shah, M.B.Jang, H.H.Zhang, Q.David Stout, C.Halpert, J.R.

(2013) Arch.Biochem.Biophys. 530: 64-72

  • DOI: 10.1016/j.abb.2012.12.016

  • PubMed Abstract: 
  • Prior X-ray crystal structures of cytochrome P450 2B4 revealed the pivotal role of rearrangement of the side chains of residues F206 and F297 in the active site in accommodating various inhibitors or substrates. To explore the role of these residues, ...

    Prior X-ray crystal structures of cytochrome P450 2B4 revealed the pivotal role of rearrangement of the side chains of residues F206 and F297 in the active site in accommodating various inhibitors or substrates. To explore the role of these residues, 2B4 F206A and F297A were created by site-directed mutagenesis and characterized functionally. The structure of F297A with clopidogrel demonstrated the reorientation of the ligand such that the methyl ester group is oriented toward the heme, whereas the thiophene moiety now extends to the additional void in the F297A mutant. Most interestingly, movement of the I helix and several amino acid side chains within the active site was observed in apparent response to the altered binding orientation. Results of flexible docking using the 2B4 wild type or the F297A-virtual mutant positioned either the thiophene or chlorophenyl group closer to heme. However, docking of clopidogrel using the real F297A mutant or a virtual mutant with the I-helix re-positioned oriented clopidogrel preferentially with either the methyl ester or the chlorophenyl group closest to heme. The study provides insight into how the altered active site adapts to accommodate and interact with the substrate in a distinct orientation while maintaining the overall closed protein conformation.


    Organizational Affiliation

    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 2B4
A
479Oryctolagus cuniculusGene Names: CYP2B4
EC: 1.14.14.1
Find proteins for P00178 (Oryctolagus cuniculus)
Go to UniProtKB:  P00178
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CGE
Query on CGE

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Download CCD File 
A
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
CM5
Query on CM5

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Download CCD File 
A
5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE; CYMAL-5
C23 H42 O11
RVTGFZGNOSKUDA-ZNGNCRBCSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.233 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 91.385α = 90.00
b = 91.385β = 90.00
c = 152.286γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALAdata scaling
Blu-Icedata collection
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-01-23
    Type: Database references
  • Version 1.2: 2013-02-20
    Type: Database references