3E4E

Human cytochrome P450 2E1 in complex with the inhibitor 4-methylpyrazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of human cytochrome P450 2E1: insights into the binding of inhibitors and both small molecular weight and fatty acid substrates.

Porubsky, P.R.Meneely, K.M.Scott, E.E.

(2008) J Biol Chem 283: 33698-33707

  • DOI: 10.1074/jbc.M805999200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Human microsomal cytochrome P-450 2E1 (CYP2E1) monooxygenates > 70 low molecular weight xenobiotic compounds, as well as much larger endogenous fatty acid signaling molecules such as arachidonic acid. In the process, CYP2E1 can generate toxic or carc ...

    Human microsomal cytochrome P-450 2E1 (CYP2E1) monooxygenates > 70 low molecular weight xenobiotic compounds, as well as much larger endogenous fatty acid signaling molecules such as arachidonic acid. In the process, CYP2E1 can generate toxic or carcinogenic compounds, as occurs with acetaminophen overdose, nitrosamines in cigarette smoke, and reactive oxygen species from uncoupled catalysis. Thus, the diverse roles that CYP2E1 has in normal physiology, toxicity, and drug metabolism are related to its ability to metabolize diverse classes of ligands, but the structural basis for this was previously unknown. Structures of human CYP2E1 have been solved to 2.2 angstroms for an indazole complex and 2.6 angstroms for a 4-methylpyrazole complex. Both inhibitors bind to the heme iron and hydrogen bond to Thr303 within the active site. Complementing its small molecular weight substrates, the hydrophobic CYP2E1 active site is the smallest yet observed for a human cytochrome P-450. The CYP2E1 active site also has two adjacent voids: one enclosed above the I helix and the other forming a channel to the protein surface. Minor repositioning of the Phe478 aromatic ring that separates the active site and access channel would allow the carboxylate of fatty acid substrates to interact with conserved 216QXXNN220 residues in the access channel while positioning the hydrocarbon terminus in the active site, consistent with experimentally observed omega-1 hydroxylation of saturated fatty acids. Thus, these structures provide insights into the ability of CYP2E1 to effectively bind and metabolize both small molecule substrates and fatty acids.


    Organizational Affiliation

    Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 2E1A, B476Homo sapiensMutation(s): 0 
Gene Names: CYP2E1CYP2E
EC: 1.14.14.1 (PDB Primary Data), 1.14.13 (UniProt)
Find proteins for P05181 (Homo sapiens)
Explore P05181 
Go to UniProtKB:  P05181
NIH Common Fund Data Resources
PHAROS  P05181
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
4PZ
Query on 4PZ

Download CCD File 
A, B
4-methyl-1H-pyrazole
C4 H6 N2
RIKMMFOAQPJVMX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.193α = 90
b = 71.193β = 90
c = 225.888γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance