5E0E

Crystal Structure of Cytochrome P450 2B37 from Desert Woodrat in complex with 4-(4-chlorophenyl)imidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-Function Analysis of Mammalian CYP2B Enzymes Using 7-Substituted Coumarin Derivatives as Probes: Utility of Crystal Structures and Molecular Modeling in Understanding Xenobiotic Metabolism.

Shah, M.B.Liu, J.Huo, L.Zhang, Q.Dearing, M.D.Wilderman, P.R.Szklarz, G.D.Stout, C.D.Halpert, J.R.

(2016) Mol.Pharmacol. 89: 435-445

  • DOI: 10.1124/mol.115.102111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of CYP2B35 and CYP2B37 from the desert woodrat were solved in complex with 4-(4-chlorophenyl)imidazole (4-CPI). The closed conformation of CYP2B35 contained two molecules of 4-CPI within the active site, whereas the CYP2B37 structu ...

    Crystal structures of CYP2B35 and CYP2B37 from the desert woodrat were solved in complex with 4-(4-chlorophenyl)imidazole (4-CPI). The closed conformation of CYP2B35 contained two molecules of 4-CPI within the active site, whereas the CYP2B37 structure demonstrated an open conformation with three 4-CPI molecules, one within the active site and the other two in the substrate access channel. To probe structure-function relationships of CYP2B35, CYP2B37, and the related CYP2B36, we tested the O-dealkylation of three series of related substrates-namely, 7-alkoxycoumarins, 7-alkoxy-4-(trifluoromethyl)coumarins, and 7-alkoxy-4-methylcoumarins-with a C1-C7 side chain. CYP2B35 showed the highest catalytic efficiency (kcat/KM) with 7-heptoxycoumarin as a substrate, followed by 7-hexoxycoumarin. In contrast, CYP2B37 showed the highest catalytic efficiency with 7-ethoxy-4-(trifluoromethyl)coumarin (7-EFC), followed by 7-methoxy-4-(trifluoromethyl)coumarin (7-MFC). CYP2B35 had no dealkylation activity with 7-MFC or 7-EFC. Furthermore, the new CYP2B-4-CPI-bound structures were used as templates for docking the 7-substituted coumarin derivatives, which revealed orientations consistent with the functional studies. In addition, the observation of multiple -Cl and -NH-π interactions of 4-CPI with the aromatic side chains in the CYP2B35 and CYP2B37 structures provides insight into the influence of such functional groups on CYP2B ligand binding affinity and specificity. To conclude, structural, computational, and functional analysis revealed striking differences between the active sites of CYP2B35 and CYP2B37 that will aid in the elucidation of new structure-activity relationships.


    Organizational Affiliation

    School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.) manish.shah@uconn.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 family 2 subfamily B
A
463Neotoma lepidaMutation(s): 0 
Gene Names: CYP2B
Find proteins for J9JD75 (Neotoma lepida)
Go to UniProtKB:  J9JD75
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
CPZ
Query on CPZ

Download SDF File 
Download CCD File 
A
4-(4-CHLOROPHENYL)IMIDAZOLE
C9 H7 Cl N2
DVKIFCXVRCGAEE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.212 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 144.770α = 90.00
b = 144.770β = 90.00
c = 104.470γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesIOS 1256840

Revision History 

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Database references, Derived calculations