8ZNN | pdb_00008znn

X-ray structure of human PPAR delta ligand binding domain in complex with a synthetic agonist 16a

PDB DOI: https://doi.org/10.2210/pdb8ZNN/pdb

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

Deposited: 2024-05-27 Released: 2025-12-24
Deposition Author(s): Dai, L., Sun, H., Feng, Z.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.227 (Depositor), 0.228 (DCC)
R-Value Work:
0.190 (Depositor), 0.192 (DCC)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Design, Synthesis, and Biological Evaluation of Arylimidazole Derivatives as Potent PPARd Agonists for the Treatment of Renal Fibrosis

Feng, Z., Sun, H., Dai, L.

To be published.

Macromolecule Content

Total Structure Weight: 31.39 kDa
Atom Count: 2,386
Modeled Residue Count: 260
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor delta	A	270	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q03181
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D86 (Subject of Investigation/LOI) Query on A1D86 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	6-[2-[[2-[4-(trifluoromethyloxy)phenyl]benzimidazol-1-yl]methyl]phenoxy]hexanoic acid C₂₇ H₂₅ F₃ N₂ O₄ CIJJQZAOSIHXTJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.227 (Depositor), 0.228 (DCC)
R-Value Work: 0.190 (Depositor), 0.192 (DCC)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.228	α = 90
b = 93.553	β = 90
c = 95.962	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	China	--

Revision History (Full details and data files)

Version 1.0: 2025-12-24
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.