4RRT

Crystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in complex with (+)-3-carene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Biophysical Characterization of Human Cytochromes P450 2B6 and 2A6 Bound to Volatile Hydrocarbons: Analysis and Comparison.

Shah, M.B.Wilderman, P.R.Liu, J.Jang, H.H.Zhang, Q.Stout, C.D.Halpert, J.R.

(2015) Mol.Pharmacol. 87: 649-659

  • DOI: 10.1124/mol.114.097014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • X-ray crystal structures of complexes of cytochromes CYP2B6 and CYP2A6 with the monoterpene sabinene revealed two distinct binding modes in the active sites. In CYP2B6, sabinene positioned itself with the putative oxidation site located closer to the ...

    X-ray crystal structures of complexes of cytochromes CYP2B6 and CYP2A6 with the monoterpene sabinene revealed two distinct binding modes in the active sites. In CYP2B6, sabinene positioned itself with the putative oxidation site located closer to the heme iron. In contrast, sabinene was found in an alternate conformation in the more compact CYP2A6, where the larger hydrophobic side chains resulted in a significantly reduced active-site cavity. Furthermore, results from isothermal titration calorimetry indicated a much more substantial contribution of favorable enthalpy to sabinene binding to CYP2B6 as opposed to CYP2A6, consistent with the previous observations with (+)-α-pinene. Structural analysis of CYP2B6 complexes with sabinene and the structurally similar (3)-carene and comparison with previously solved structures revealed how the movement of the F206 side chain influences the volume of the binding pocket. In addition, retrospective analysis of prior structures revealed that ligands containing -Cl and -NH functional groups adopted a distinct orientation in the CYP2B active site compared with other ligands. This binding mode may reflect the formation of Cl-π or NH-π bonds with aromatic rings in the active site, which serve as important contributors to protein-ligand binding affinity and specificity. Overall, the findings from multiple techniques illustrate how drugs metabolizing CYP2B6 and CYP2A6 handle a common hydrocarbon found in the environment. The study also provides insight into the role of specific functional groups of the ligand that may influence the binding to CYP2B6.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, The University of Connecticut, Storrs, Connecticut (M.B.S., P.R.W., J.L., J.R.H.); School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea (H.-H.J.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.) manish.shah@uconn.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 2B6
A, B
476Homo sapiensMutation(s): 10 
Gene Names: CYP2B6
EC: 1.14.13.-
Find proteins for P20813 (Homo sapiens)
Go to Gene View: CYP2B6
Go to UniProtKB:  P20813
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
3V4
Query on 3V4

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Download CCD File 
A, B
(+)-3-carene
(1R,6S)-3,7,7-trimethylbicyclo[4.1.0]hept-3-ene
C10 H16
BQOFWKZOCNGFEC-DTWKUNHWSA-N
 Ligand Interaction
CM5
Query on CM5

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Download CCD File 
A, B
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, B
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: 2.2 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.170 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 78.070α = 90.00
b = 78.070β = 90.00
c = 203.081γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
Blu-Icedata collection
REFMACrefinement
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-11-06 
  • Released Date: 2015-01-28 
  • Deposition Author(s): Shah, M.B.

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-03-11
    Type: Database references