7VWE

Human peroxisome proliferator-activated receptor (PPAR) delta ligand binding domain in complex with a synthetic partial agonist JK122

• PDB DOI: https://doi.org/10.2210/pdb7VWE/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-11-10 Released: 2022-02-09 
• Deposition Author(s): Oyama, T., Miyachi, H.
• Funding Organization(s): Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.232 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 

Starting Model: experimental

Literature

Crystal structures of the ligand-binding domain of human peroxisome proliferator-activated receptor delta in complexes with phenylpropanoic acid derivatives and a pyridine carboxylic acid derivative.

Oyama, T., Takiguchi, K., Miyachi, H.

(2022) Acta Crystallogr F Struct Biol Commun 78: 81-87

• DOI: https://doi.org/10.1107/S2053230X22000449

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 64.65 kDa 
• Atom Count: 4,257 
• Modelled Residue Count: 513 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor delta	A, B	276	Homo sapiens	Mutation(s): 0  Gene Names: PPARD, NR1C2, PPARB
UniProt & NIH Common Fund Data Resources
Find proteins for Q03181 (Homo sapiens) Explore Q03181  Go to UniProtKB:  Q03181
PHAROS:  Q03181 GTEx:  ENSG00000112033

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
81O (Subject of Investigation/LOI)	D [auth A], F [auth B]	5-[4-butoxy-3-[[[2-fluoranyl-4-(trifluoromethyl)phenyl]carbonylamino]methyl]phenyl]-4,6-dimethyl-pyridine-3-carboxylic acid C27 H26 F4 N2 O4 UNUJRJCEJXKUFP-UHFFFAOYSA-N
B7G (Subject of Investigation/LOI)	C [auth A], E [auth B]	heptyl beta-D-glucopyranoside C13 H26 O6 NIDYWHLDTIVRJT-UJPOAAIJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.232 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.123	α = 90
b = 92.303	β = 98.055
c = 96.088	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-09 
Deposition Author(s): Oyama, T., Miyachi, H.

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Funding Organization	Location	Grant Number
Japan Science and Technology		JPMJTM20NM

Revision History  

• Version 1.0: 2022-02-09
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description