Structure of human cytochrome P450 CYP2C9

Experimental Data Snapshot

  • Resolution: 2.55 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.225 

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Crystal Structure of Human Cytochrome P450 2C9 with Bound Warfarin

Williams, P.A.Cosme, J.Ward, A.Angove, H.C.Matak Vinkovic, D.Jhoti, H.

(2003) Nature 424: 464

  • DOI: https://doi.org/10.1038/nature01862
  • Primary Citation of Related Structures:  
    1OG2, 1OG5

  • PubMed Abstract: 

    Cytochrome P450 proteins (CYP450s) are membrane-associated haem proteins that metabolize physiologically important compounds in many species of microorganisms, plants and animals. Mammalian CYP450s recognize and metabolize diverse xenobiotics such as drug molecules, environmental compounds and pollutants. Human CYP450 proteins CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A4 are the major drug-metabolizing isoforms, and contribute to the oxidative metabolism of more than 90% of the drugs in current clinical use. Polymorphic variants have also been reported for some CYP450 isoforms, which has implications for the efficacy of drugs in individuals, and for the co-administration of drugs. The molecular basis of drug recognition by human CYP450s, however, has remained elusive. Here we describe the crystal structure of a human CYP450, CYP2C9, both unliganded and in complex with the anti-coagulant drug warfarin. The structure defines unanticipated interactions between CYP2C9 and warfarin, and reveals a new binding pocket. The binding mode of warfarin suggests that CYP2C9 may undergo an allosteric mechanism during its function. The newly discovered binding pocket also suggests that CYP2C9 may simultaneously accommodate multiple ligands during its biological function, and provides a possible molecular basis for understanding complex drug-drug interactions.

  • Organizational Affiliation

    Astex Technology, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
475Homo sapiensMutation(s): 7 
EC: (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P11712 (Homo sapiens)
Explore P11712 
Go to UniProtKB:  P11712
PHAROS:  P11712
GTEx:  ENSG00000138109 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11712
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.55 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.225 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.757α = 90
b = 164.757β = 90
c = 110.762γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-17
    Type: Initial release
  • Version 1.1: 2011-11-09
    Changes: Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations