3H0A

Crystal Structure of Peroxisome Proliferator-Activated Receptor Gamma (PPARg) and Retinoic Acid Receptor Alpha (RXRa) in Complex with 9-cis Retinoic Acid, Co-activator Peptide, and a Partial Agonist

• PDB DOI:  https://doi.org/10.2210/pdb3H0A/pdb

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


• Deposited: 2009-04-08 Released: 2009-06-09 
• Deposition Author(s): Wang, Z., Sudom, A., Walker, N.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.342 
• R-Value Work: 0.246 
• R-Value Observed: 0.251 

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 of 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: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.3 kDa 
• Atom Count: 4,147 
• Modelled Residue Count: 498 
• Deposited Residue Count: 524 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor RXR-alpha	A	228	Homo sapiens	Mutation(s): 0  Gene Names: RXRA, NR2B1
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens) Explore P19793  Go to UniProtKB:  P19793
PHAROS:  P19793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	B [auth D]	272	Homo sapiens	Mutation(s): 0  Gene Names: PPARG, NR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
PHAROS:  P37231

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1, Co-activator Peptide	C [auth B], D [auth E]	12	Homo sapiens	Mutation(s): 0  Gene Names: NCOA1, BHLHE74, SRC1 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D30	F [auth D]	[(4-{[2-(pent-2-yn-1-yloxy)-4-{[4-(trifluoromethyl)phenoxy]methyl}phenyl]sulfanyl}-5,6,7,8-tetrahydronaphthalen-1-yl)oxy]acetic acid C31 H29 F3 O5 S SIHDSSYICQEWRS-UHFFFAOYSA-N
9RA	E [auth A]	4-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydronaphthalen-2-yl)ethenyl]benzoic acid C24 H28 O2 NAVMQTYZDKMPEU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9RA	BindingDB:  3H0A	Ki: min: 5.9, max: 379 (nM) from 15 assay(s)
		Kd: min: 7, max: 1890 (nM) from 13 assay(s)
		IC50: 632 (nM) from 1 assay(s)
		EC50: min: 2.7, max: 149 (nM) from 22 assay(s)
D30	Binding MOAD:  3H0A	Ki: 33 (nM) from 1 assay(s)
	PDBBind:  3H0A	Ki: 33 (nM) from 1 assay(s)
	BindingDB:  3H0A	Ki: 33 (nM) from 1 assay(s)
		EC50: 160 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.342 
• R-Value Work: 0.246 
• R-Value Observed: 0.251 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.258	α = 90
b = 53.825	β = 107.74
c = 67.108	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: 2009-06-09 
Deposition Author(s): Wang, Z., Sudom, A., Walker, N.P.

Revision History  

• Version 1.0: 2009-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-04-02
  Changes: Source and taxonomy