6VLT

Crystal Structure of Human P450 2C9*2 Genetic Variant in Complex with Losartan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.159 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure of Cytochrome P450 2C9*2 in Complex with Losartan: Insights into the Effect of Genetic Polymorphism.

Parikh, S.J.Evans, C.M.Obi, J.O.Zhang, Q.Maekawa, K.Glass, K.C.Shah, M.B.

(2020) Mol Pharmacol 98: 529-539

  • DOI: https://doi.org/10.1124/molpharm.120.000042
  • Primary Citation of Related Structures:  
    6VLT

  • PubMed Abstract: 

    The human CYP2C9 plays a crucial role in the metabolic clearance of a wide range of clinical therapeutics. The *2 allele is a prevalent genetic variation in CYP2C9 that is found in various populations. A marked reduction of catalytic activity toward many important drug substrates has been demonstrated by CYP2C9*2, which represents an amino acid variation at position 144 from arginine to cysteine. The crystal structure of CYP2C9*2 in complex with an antihypertensive drug losartan was solved using X-ray crystallography at 3.1-Å resolution. The Arg144Cys variation in the *2 complex disrupts the hydrogen-bonding interactions that were observed between the side chain of arginine and neighboring residues in the losartan complex of CYP2C9 and the wild-type (WT) ligand-free structure. The conformation of several secondary structural elements is affected, thereby altering the binding and orientation of drug and important amino acid side chains in the distal active site cavity. The new structure revealed distinct interactions of losartan in the compact active site of CYP2C9*2 and differed in occupancy at the other binding sites previously identified in the WT-losartan complex. Furthermore, the binding studies in solution using losartan illustrated lower activity of the CYP2C9*2 compared with the WT. Together, the findings yield valuable insights into the decreased hydroxylation activity of losartan in patients carrying CYP2C9*2 allele and provide a useful framework to investigate the effect of a single-nucleotide polymorphism that leads to altered metabolism of diverse drug substrates. SIGNIFICANCE STATEMENT: The *2 allele of the human drug-metabolizing enzyme CYP2C9 is found in different populations and results in significantly reduced activity toward various drug substrates. How the CYP2C9*2 variant induces altered drug metabolism is poorly understood given that the Arg144Cys variation is located far away from the active site. This work yield insight into the effect of distal variation using multitude of techniques that include X-ray crystallography, isothermal titration calorimetry, enzymatic characterization, and computational studies.


  • Organizational Affiliation

    Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York (S.J.P., C.M.E., J.O.O., K.C.G., M.B.S.); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (Q.Z.); and Department of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts, Kodo, Kyotanabe, Kyoto, Japan (K.M.).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 2C9
A, B, C, D, E
A, B, C, D, E, F, G, H
476Homo sapiensMutation(s): 2 
Gene Names: CYP2C9CYP2C10
EC: 1.14.14.1 (PDB Primary Data), 1.14.14.53 (PDB Primary Data), 1.14.14.51 (PDB Primary Data), 1.14.14.52 (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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
BA [auth G]
GA [auth H]
I [auth A]
K [auth B]
M [auth C]
BA [auth G],
GA [auth H],
I [auth A],
K [auth B],
M [auth C],
O [auth D],
R [auth E],
W [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
CM5
Query on CM5

Download Ideal Coordinates CCD File 
AA [auth G]
DA [auth G]
FA [auth H]
IA [auth H]
Q [auth E]
AA [auth G],
DA [auth G],
FA [auth H],
IA [auth H],
Q [auth E],
T [auth E],
V [auth F],
Y [auth F]
5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
C23 H42 O11
RVTGFZGNOSKUDA-ZNGNCRBCSA-N
LSN (Subject of Investigation/LOI)
Query on LSN

Download Ideal Coordinates CCD File 
CA [auth G]
HA [auth H]
J [auth A]
L [auth B]
N [auth C]
CA [auth G],
HA [auth H],
J [auth A],
L [auth B],
N [auth C],
P [auth D],
S [auth E],
X [auth F]
[2-butyl-5-chloranyl-3-[[4-[2-(2H-1,2,3,4-tetrazol-5-yl)phenyl]phenyl]methyl]imidazol-4-yl]methanol
C22 H23 Cl N6 O
PSIFNNKUMBGKDQ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
EA [auth G],
U [auth E],
Z [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.159 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 238.1α = 90
b = 238.1β = 90
c = 109.851γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata processing
BALBESphasing
Cootmodel building
iMOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2020-09-30 
  • Deposition Author(s): Shah, M.B.

Funding OrganizationLocationGrant Number
American Heart AssociationUnited States19AIREA34450040

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.3: 2024-04-03
    Changes: Refinement description