Microsomal P450 2A6 with the inhibitor Adrithiol bound

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

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Synthetic Inhibitors of Cytochrome P-450 2A6: Inhibitory Activity, Difference Spectra, Mechanism of Inhibition, and Protein Cocrystallization.

Yano, J.K.Denton, T.T.Cerny, M.A.Zhang, X.Johnson, E.F.Cashman, J.R.

(2006) J Med Chem 49: 6987-7001

  • DOI: https://doi.org/10.1021/jm060519r
  • Primary Citation of Related Structures:  
    2FDU, 2FDV, 2FDW, 2FDY

  • PubMed Abstract: 

    A series of 3-heteroaromatic analogues of nicotine were synthesized to delineate structural and mechanistic requirements for selectively inhibiting human cytochrome P450 (CYP) 2A6. Thiophene, substituted thiophene, furan, substituted furan, acetylene, imidazole, substituted imidazole, thiazole, pyrazole, substituted pyrazole, and aliphatic and isoxazol moieties were used to replace the N-methylpyrrolidine ring of nicotine. A number of potent inhibitors were identified, and several exhibited high selectivity for CYP2A6 relative to CYP2E1, -3A4, -2B6, -2C9, -2C19, and -2D6. The majority of these inhibitors elicited type II difference spectra indicating the formation of a coordinate covalent bond to the heme iron. The majority of inhibitors were reversible inhibitors although several mechanism-based inactivators were identified. Most of the inhibitors were also relatively metabolically stable. X-ray crystal structures of CYP2A6 cocrystallized with three furan analogues bearing methanamino side chains indicated that the amine side chain coordinated to the heme iron. The pyridyl moiety was positioned to accept a hydrogen bond from Asn297, and all three inhibitors exhibited orthogonal aromatic-aromatic interactions with protein side chains. For comparison, the cocrystal structure of 4,4'-dipyridyl disulfide was also obtained and showed that the pyridine moiety could assume a different orientation than that observed for the 3-heteroaromatic pyridines examined. For the 3-heteroromatic pyridines, N-methyl and N,N-dimethyl amino groups increased the apparent Ki and distorted helix I of the protein. Substitution of a phenyl ring for the pyridyl ring also increased the apparent Ki, which is likely to reflect the loss of the hydrogen bonding interaction with Asn297. In contrast, inhibitory potency for other P450s was increased, and the selectivity of the phenyl analogues for CYP2A6 was decreased relative to the pyridyl compounds. The results suggest that inhibitors that compliment the active site features of CYP2A6 can exhibit significant selectivity for CYP2A6 relative to other human liver drug-metabolizing P450s.

  • Organizational Affiliation

    Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, California 92121, 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: CYP2A6
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
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
L [auth C],
N [auth D]
C34 H32 Fe N4 O4
Query on D4G

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
M [auth C],
O [auth D]
C10 H8 N2 S2
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.197α = 90
b = 156.62β = 91.79
c = 103.997γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description