5Y7X

Human Peroxisome proliferator-activated receptor (PPAR) delta in complexed with a potent and selective agonist

• PDB DOI: https://doi.org/10.2210/pdb5Y7X/pdb

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


• Deposited: 2017-08-18 Released: 2018-08-01 
• Deposition Author(s): Kim, H.L., Chin, J.W., Cho, S.J., Song, J.Y., Yoon, H.S., Bae, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.231 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

Design, synthesis, and the X-ray co-crystal structure of Highly Potent, Selective, and Orally Bioavailable, Novel Peroxisome Proliferator-Activated Receptor delta Agonists

Chin, J.W., Cho, S.J.

To be published.

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)

Macromolecule Content

• Total Structure Weight: 68.35 kDa 
• Atom Count: 4,546 
• Modelled Residue Count: 520 
• Deposited Residue Count: 584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor delta	A, B	292	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8RR	C [auth A], H [auth B]	2-[2-methyl-4-[[4-methyl-2-[4-(trifluoromethyl)phenyl]-1,3-selenazol-5-yl]methylsulfanyl]phenoxy]ethanoic acid C21 H18 F3 N O3 S Se FLCJPWUNOIWRCO-UHFFFAOYSA-N
JZR	G [auth A], J [auth B]	hexyl beta-D-glucopyranoside C12 H24 O6 JVAZJLFFSJARQM-RMPHRYRLSA-N
PGO	F [auth A]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	E [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.231 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.766	α = 90
b = 93.896	β = 97.4
c = 96.871	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
PHENIX	phasing
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-01 
Deposition Author(s): Kim, H.L., Chin, J.W., Cho, S.J., Song, J.Y., Yoon, H.S., Bae, J.H.

Revision History  

• Version 1.0: 2018-08-01
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary