2NNH

CYP2C8dH complexed with 2 molecules of 9-cis retinoic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.244 

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This is version 1.2 of the entry. See complete history. 


Literature

Determinants of cytochrome P450 2C8 substrate binding: structures of complexes with montelukast, troglitazone, felodipine, and 9-cis-retinoic acid.

Schoch, G.A., Yano, J.K., Sansen, S., Dansette, P.M., Stout, C.D., Johnson, E.F.

(2008) J Biol Chem 283: 17227-17237

  • DOI: 10.1074/jbc.M802180200
  • Primary Citation of Related Structures:  
    2NNH, 2NNI, 2NNJ, 2VN0

  • PubMed Abstract: 

    • Although a crystal structure and a pharmacophore model are available for cytochrome P450 2C8, the role of protein flexibility and specific ligand-protein interactions that govern substrate binding are poorly understood. X-ray crystal structures of P450 2C8 complexed with montelukast (2 ...

    Although a crystal structure and a pharmacophore model are available for cytochrome P450 2C8, the role of protein flexibility and specific ligand-protein interactions that govern substrate binding are poorly understood. X-ray crystal structures of P450 2C8 complexed with montelukast (2.8 A), troglitazone (2.7 A), felodipine (2.3 A), and 9-cis-retinoic acid (2.6 A) were determined to examine ligand-protein interactions for these chemically diverse compounds. Montelukast is a relatively large anionic inhibitor that exhibits a tripartite structure and complements the size and shape of the active-site cavity. The inhibitor troglitazone occupies the upper portion of the active-site cavity, leaving a substantial part of the cavity unoccupied. The smaller neutral felodipine molecule is sequestered with its dichlorophenyl group positioned close to the heme iron, and water molecules fill the distal portion of the cavity. The structure of the 9-cis-retinoic acid complex reveals that two substrate molecules bind simultaneously in the active site of P450 2C8. A second molecule of 9-cis-retinoic acid is located above the proximal molecule and can restrain the position of the latter for more efficient oxygenation. Solution binding studies do not discriminate between cooperative and noncooperative models for multiple substrate binding. The complexes with structurally distinct ligands further demonstrate the conformational adaptability of active site-constituting residues, especially Arg-241, that can reorient in the active-site cavity to stabilize a negatively charged functional group and define two spatially distinct binding sites for anionic moieties of substrates.

    Organizational Affiliation: 

    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450 2C8A, B476Homo sapiensMutation(s): 0 
Gene Names: CYP2C8
EC: 1.14.14.1
UniProt & NIH Common Fund Data Resources
Find proteins for P10632 (Homo sapiens)
Explore P10632 
Go to UniProtKB:  P10632
PHAROS:  P10632
GTEx:  ENSG00000138115 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10632
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.244 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.81α = 90
b = 163.62β = 90
c = 73.555γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2016-11-16
    Changes: Non-polymer description