Human cytochrome P450 2E1 in complex with the inhibitor indazole

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

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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: https://doi.org/10.1074/jbc.M805999200
  • Primary Citation of Related Structures:  
    3E4E, 3E6I

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 2E1
A, B
476Homo sapiensMutation(s): 0 
Gene Names: CYP2E1CYP2E
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P05181 (Homo sapiens)
Explore P05181 
Go to UniProtKB:  P05181
PHAROS:  P05181
GTEx:  ENSG00000130649 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05181
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.083α = 90
b = 71.083β = 90
c = 225.17γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description