3PEQ | pdb_00003peq

PPARd complexed with a phenoxyacetic acid partial agonist

• PDB DOI: https://doi.org/10.2210/pdb3PEQ/pdb

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


• Deposited: 2010-10-27 Released: 2011-10-12 
• Deposition Author(s): Lambert, M.H., Evans, K.A., Shearer, B.G., Wisnoski, D.D., Shi, D., Jin, J., Rivero, R.A., Sparks, S.M., Winegar, D.A., Billin, A.N., Britt, C., Way, J.M., Leesnitzer, L.M., Merrihew, R.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.237 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Phenoxyacetic acid PPARd partial agonists for the treatment of type 2 diabetes: synthesis, optimization, and in vivo efficacy

Evans, K.A., Shearer, B.G., Wisnoski, D.D., Shi, D., Sparks, S.M., Sternbach, D.D., Winegar, D.A., Billin, A.N., Britt, C., Way, J.M., Epperly, A.H., Leesnitzer, L.M., Merrihew, R.V., Xu, R.X., Lambert, M.H., Jin, J.

(2011) Bioorg Med Chem Lett 21: 2345-2350

• PubMed: 21414782 
• DOI: https://doi.org/10.1016/j.bmcl.2011.02.077
• Primary Citation Related Structures: 
  3PEQ


• PubMed Abstract: 
  

  A series of phenoxyacetic acids as subtype selective and potent hPPARδ partial agonists is described. Many analogues were readily accessible via a single solution-phase synthetic route which resulted in the rapid identification of key structure-activity relationships (SAR), and the discovery of two potent exemplars which were further evaluated in vivo. Details of the SAR, optimization, and in vivo efficacy of this series are presented herein.

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Organizational Affiliation: 
• Discovery Medicinal Chemistry, Discovery Research, GlaxoSmithKline Pharmaceuticals, 1250 South Collegeville Road, PO Box 5089, Collegeville, PA 19426-0989, United States. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.69 kDa 
• Atom Count: 4,391 
• Modeled Residue Count: 512 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor delta	A, B	271	Homo sapiens	Mutation(s): 0  Gene Names: NR1C2, PPARB, PPARD
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3EQ	C [auth A], J [auth B]	[(4-{butyl[2-methyl-4'-(methylsulfanyl)biphenyl-3-yl]sulfamoyl}naphthalen-1-yl)oxy]acetic acid C30 H31 N O5 S2 XUMLNRUSPQDSIN-UHFFFAOYSA-N
JZR	D [auth A], E [auth A], K [auth B]	hexyl beta-D-glucopyranoside C12 H24 O6 JVAZJLFFSJARQM-RMPHRYRLSA-N
IOD	F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.237 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.472	α = 90
b = 95.535	β = 97.76
c = 96.537	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Lambert, M.H., Evans, K.A., Shearer, B.G., Wisnoski, D.D., Shi, D., Jin, J., Rivero, R.A., Sparks, S.M., Winegar, D.A., Billin, A.N., Britt, C., Way, J.M., Leesnitzer, L.M., Merrihew, R.V.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2014-10-08
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary