2ZNQ

Human PPAR delta ligand binding domain in complex with a synthetic agonist TIPP401

• PDB DOI: https://doi.org/10.2210/pdb2ZNQ/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2008-04-30 Released: 2009-05-05 
• Deposition Author(s): Oyama, T., Hirakawa, Y., Nagasawa, N., Miyachi, H., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.276 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.47 kDa 
• Atom Count: 4,395 
• Modelled Residue Count: 522 
• 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
401	D [auth A], F [auth B]	(2S)-2-{3-[({[2-fluoro-4-(trifluoromethyl)phenyl]carbonyl}amino)methyl]-4-methoxybenzyl}butanoic acid C21 H21 F4 N O4 BDLLIPYDNFENMY-ZDUSSCGKSA-N
B7G	C [auth A], E [auth B]	heptyl beta-D-glucopyranoside C13 H26 O6 NIDYWHLDTIVRJT-UJPOAAIJSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
401	BindingDB:  2ZNQ	EC50: min: 12, max: 29 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.276 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.172	α = 90
b = 91.947	β = 98.01
c = 96.361	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-05 
Deposition Author(s): Oyama, T., Hirakawa, Y., Nagasawa, N., Miyachi, H., Morikawa, K.

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-04-11
  Changes: Database references
• Version 1.3: 2016-03-02
  Changes: Structure summary
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.5: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary