2HWQ

Structural basis for the structure-activity relationships of Peroxisome Proliferator-Activated Receptor agonists

• PDB DOI: https://doi.org/10.2210/pdb2HWQ/pdb

• Classification: LIGAND BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-08-01 Released: 2007-08-07 
• Deposition Author(s): Peng, Y.H., Lu, I.L., Mahindroo, N., Lin, C.H., Hsieh, H.P., Wu, S.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.265 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the structure-activity relationships of peroxisome proliferator-activated receptor agonists

Mahindroo, N., Peng, Y.H., Lin, C.H., Tan, U.K., Prakash, E., Lien, T.W., Lu, I.L., Lee, H.J., Hsu, J.T.A., Chen, X., Liao, C.C., Lyu, P.C., Chao, Y.S., Wu, S.Y., Hsieh, H.P.

(2006) J Med Chem 49: 6421-6424

• PubMed: 17034149 
• DOI: https://doi.org/10.1021/jm060663c
• Primary Citation of Related Structures:  
  2HWQ, 2HWR


• PubMed Abstract: 
  

  Type 2 diabetes has rapidly reached an epidemic proportion becoming a major threat to global public health. PPAR agonists have emerged as a leading class of oral antidiabetic drugs. We report a structure biology analysis of novel indole-based PPAR agonists to explain the structure-activity relationships and present a critical analysis of reasons for change in selectivity with change in the orientation of the same scaffolds. The results would be helpful in designing novel PPAR agonists.

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Organizational Affiliation: 

Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, Republic of China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.52 kDa 
• Atom Count: 4,347 
• Modelled Residue Count: 514 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	271	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
PHAROS:  P37231 GTEx:  ENSG00000132170

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DRY	C [auth A]	[(1-{3-[(6-BENZOYL-1-PROPYL-2-NAPHTHYL)OXY]PROPYL}-1H-INDOL-5-YL)OXY]ACETIC ACID C33 H31 N O5 CIJITCGUOBZSCP-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DRY	BindingDB:  2HWQ	EC50: 2210 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.265 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.015	α = 90
b = 88.671	β = 90.24
c = 58.024	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-07 
Deposition Author(s): Peng, Y.H., Lu, I.L., Mahindroo, N., Lin, C.H., Hsieh, H.P., Wu, S.Y.

Revision History  

• Version 1.0: 2007-08-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description