Human Cytochrome P450 2A6 in complex with nicotine

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

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Nicotine and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone binding and access channel in human cytochrome P450 2A6 and 2A13 enzymes.

DeVore, N.M.Scott, E.E.

(2012) J Biol Chem 287: 26576-26585

  • DOI: https://doi.org/10.1074/jbc.M112.372813
  • Primary Citation of Related Structures:  
    4EJG, 4EJH, 4EJI, 4EJJ

  • PubMed Abstract: 

    Cytochromes P450 (CYP) from the 2A subfamily are known for their roles in the metabolism of nicotine, the addictive agent in tobacco, and activation of the tobacco procarcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Although both the hepatic CYP2A6 and respiratory CYP2A13 enzymes metabolize these compounds, CYP2A13 does so with much higher catalytic efficiency, but the structural basis for this has been unclear. X-ray structures of nicotine complexes with CYP2A13 (2.5 Å) and CYP2A6 (2.3 Å) yield a structural rationale for the preferential binding of nicotine to CYP2A13. Additional structures of CYP2A13 with NNK reveal either a single NNK molecule in the active site with orientations corresponding to metabolites known to form DNA adducts and initiate lung cancer (2.35 Å) or with two molecules of NNK bound (2.1 Å): one in the active site and one in a more distal staging site. Finally, in contrast to prior CYP2A structures with enclosed active sites, CYP2A13 conformations were solved that adopt both open and intermediate conformations resulting from an ∼2.5 Å movement of the F to G helices. This channel occurs in the same region where the second, distal NNK molecule is bound, suggesting that the channel may be used for ligand entry and/or exit from the active site. Altogether these structures provide multiple new snapshots of CYP2A13 conformations that assist in understanding the binding and activation of an important human carcinogen, as well as critical comparisons in the binding of nicotine, one of the most widely used and highly addictive drugs in human use.

  • 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 2A6
A, B, C, D
476Homo sapiensMutation(s): 0 
Gene Names: CYP2A3CYP2A6
UniProt & NIH Common Fund Data Resources
Find proteins for P11509 (Homo sapiens)
Explore P11509 
Go to UniProtKB:  P11509
PHAROS:  P11509
GTEx:  ENSG00000255974 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11509
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
NCT BindingDB:  4EJJ Ki: min: 4400, max: 1.30e+5 (nM) from 3 assay(s)
Kd: min: 5.40e+4, max: 4.70e+5 (nM) from 2 assay(s)
IC50: min: 2.63e+4, max: 5.79e+5 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.214α = 90
b = 194.038β = 102.7
c = 90.266γ = 90
Software Package:
Software NamePurpose
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: 2012-06-06
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary