3GZ9 | pdb_00003gz9

Crystal Structure of Peroxisome Proliferator-Activated Receptor Delta (PPARd) in Complex with a Full Agonist

• PDB DOI: https://doi.org/10.2210/pdb3GZ9/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-04-06 Released: 2009-06-30 
• Deposition Author(s): Wang, Z., Sudom, A., Walker, N.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.245 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Identification of a PPARdelta agonist with partial agonistic activity on PPARgamma.

Connors, R.V., Wang, Z., Harrison, M., Zhang, A., Wanska, M., Hiscock, S., Fox, B., Dore, M., Labelle, M., Sudom, A., Johnstone, S., Liu, J., Walker, N.P., Chai, A., Siegler, K., Li, Y., Coward, P.

(2009) Bioorg Med Chem Lett 19: 3550-3554

• PubMed: 19464171 
• DOI: https://doi.org/10.1016/j.bmcl.2009.04.151
• Primary Citation Related Structures: 
  3GZ9, 3H0A


• PubMed Abstract: 
  

  The discovery and optimization of a series of potent PPARdelta full agonists with partial agonistic activity against PPARgamma is described.

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Organizational Affiliation: 
• Department of Chemistry, Amgen, 1120 Veterans Blvd., South San Francisco, CA 94080, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.49 kDa 
• Atom Count: 2,342 
• Modeled Residue Count: 262 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor delta	A	269	Homo sapiens	Mutation(s): 2  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
D32	C [auth A]	(2,3-dimethyl-4-{[2-(prop-2-yn-1-yloxy)-4-{[4-(trifluoromethyl)phenoxy]methyl}phenyl]sulfanyl}phenoxy)acetic acid C27 H23 F3 O5 S RMMWVBYHCKSFMW-UHFFFAOYSA-N
B7G	B [auth A]	heptyl beta-D-glucopyranoside C13 H26 O6 NIDYWHLDTIVRJT-UJPOAAIJSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
D32	BindingDB:  3GZ9	Ki: 4 (nM) from 1 assay(s)
		EC50: 54 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.245 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.577	α = 90
b = 92.129	β = 90
c = 39.555	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-30 
Deposition Author(s): Wang, Z., Sudom, A., Walker, N.P.

Revision History  

• Version 1.0: 2009-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2021-10-13
  Changes: Database references, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection