5X23 | pdb_00005x23

Crystal structure of CYP2C9 genetic variant A477T (*30) in complex with multiple losartan molecules

• PDB DOI: https://doi.org/10.2210/pdb5X23/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2017-01-30 Released: 2017-10-25 
• Deposition Author(s): Maekawa, K., Adachi, M., Shah, M.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.253 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Structural Basis of Single-Nucleotide Polymorphisms in Cytochrome P450 2C9

Maekawa, K., Adachi, M., Matsuzawa, Y., Zhang, Q., Kuroki, R., Saito, Y., Shah, M.B.

(2017) Biochemistry 56: 5476-5480

• PubMed: 28972767 
• DOI: https://doi.org/10.1021/acs.biochem.7b00795
• Primary Citation Related Structures: 
  5X23, 5X24, 5XXI


• PubMed Abstract: 
  

  Single-nucleotide polymorphisms in drug-metabolizing cytochrome P450 (CYP) enzymes are important contributors to interindividual differences in drug metabolism leading to adverse drug reactions. Despite their extensive characterization and importance in pharmacogenetics of clinical drugs, the structural basis of CYP polymorphisms has remained scant. Here we report the crystal structures of human CYP2C9 and its polymorphic variants, *3 (I359L) and *30 (A477T), with an antihypertensive drug losartan. The structures show distinct interaction and occupation of losartan in the active site, the access channel, and the peripheral binding site. The I359L substitution located far from the active site remarkably altered the residue side chains near the active site and the access channel, whereas the T477 substitution illustrated hydrogen-bonding interaction with the reoriented side chain of Q214. The results yield structural insights into the reduced catalytic activity of the CYP2C9 variants and have important implications for understanding genetic polymorphisms in CYP-mediated drug metabolism.

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Organizational Affiliation: 
• Department of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts , Kodo, Kyotanabe, Kyoto 610-0395, Japan.
Division of Medicinal Safety Science, National Institute of Health Sciences , Kamiyoga 1-18-1, Setagaya, Tokyo 158-8501, Japan.
National Institutes for Quantum and Radiological Science and Technology , 2-4 Shirane Shirakata, Tokai-mura, Ibaraki 319-1106, Japan.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.
Japan Atomic Energy Agency , 2-4 Shirane Shirakata, Tokai-mura, Ibaraki 319-1195, Japan.
Department of Pharmaceutical Sciences, University of Connecticut , Storrs, Connecticut 06267, United States.
Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences , 106 New Scotland Avenue, Albany, New York 12208, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.29 kDa 
• Atom Count: 4,026 
• Modeled Residue Count: 463 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 2C9	A	476	Homo sapiens	Mutation(s): 2  Gene Names: CYP2C9, CYP2C10 EC: 1.14.13 (PDB Primary Data), 1.14.13.80 (PDB Primary Data), 1.14.13.48 (PDB Primary Data), 1.14.13.49 (PDB Primary Data), 1.14.99.38 (PDB Primary Data), 1.14.14.1 (UniProt), 1.14.14.53 (UniProt), 1.14.14.52 (UniProt), 1.14.14.51 (UniProt) 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
LSN	C [auth A], D [auth A], E [auth A]	[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
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.253 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.952	α = 90
b = 142.273	β = 90
c = 161.831	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-10-25 
Deposition Author(s): Maekawa, K., Adachi, M., Shah, M.B.

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Funding Organization	Location	Grant Number
	Japan	KAKENHI22590054
	Japan	KAKENHI25293128

Revision History  

• Version 1.0: 2017-10-25
  Type: Initial release
  
• Version 1.1: 2017-11-01
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description