3VM4

Cytochrome P450SP alpha (CYP152B1) in complex with (R)-ibuprophen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Chiral-substrate-assisted stereoselective epoxidation catalyzed by H2O2-dependent cytochrome P450SP alpha

Fujishiro, T.Shoji, O.Kawakami, N.Watanabe, T.Sugimoto, H.Shiro, Y.Watanabe, Y.

(2012) Chem Asian J 7: 2286-2293

  • DOI: 10.1002/asia.201200250

  • PubMed Abstract: 
  • The stereoselective epoxidation of styrene was catalyzed by H(2) O(2) -dependent cytochrome P450(SPα) in the presence of carboxylic acids as decoy molecules. The stereoselectivity of styrene oxide could be altered by the nature of the decoy molecules ...

    The stereoselective epoxidation of styrene was catalyzed by H(2) O(2) -dependent cytochrome P450(SPα) in the presence of carboxylic acids as decoy molecules. The stereoselectivity of styrene oxide could be altered by the nature of the decoy molecules. In particular, the chirality at the α-positions of the decoy molecules induced a clear difference in the chirality of the product: (R)-ibuprofen enhanced the formation of (S)-styrene oxide, whereas (S)-ibuprofen preferentially afforded (R)-styrene oxide. The crystal structure of an (R)-ibuprofen-bound cytochrome P450(SPα) (resolution 1.9 Å) revealed that the carboxylate group of (R)-ibuprofen served as an acid-base catalyst to initiate the epoxidation. A docking simulation of the binding of styrene in the active site of the (R)-ibuprofen-bound form suggested that the orientation of the vinyl group of styrene in the active site agreed with the formation of (S)-styrene oxide.


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fatty acid alpha-hydroxylase
A
407Sphingomonas paucimobilisMutation(s): 0 
Find proteins for O24782 (Sphingomonas paucimobilis)
Go to UniProtKB:  O24782
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download SDF File 
Download CCD File 
A
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
IZP
Query on IZP

Download SDF File 
Download CCD File 
A
(2R)-2-[4-(2-methylpropyl)phenyl]propanoic acid
(R)-Ibuprofen
C13 H18 O2
HEFNNWSXXWATRW-SNVBAGLBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.158 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 94.390α = 90.00
b = 94.390β = 90.00
c = 112.863γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
HKL-2000data collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2013-08-14
    Type: Database references