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

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 

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This is version 1.2 of the entry. See complete history. 


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

  • DOI: 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.

    Organizational Affiliation: 

    Department of Chemistry, Amgen, 1120 Veterans Blvd., South San Francisco, CA 94080, USA. rconnors@amgen.com



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alphaA228Homo sapiensMutation(s): 0 
Gene Names: RXRA, NR2B1
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Find proteins for P19793 (Homo sapiens)
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Go to UniProtKB:  P19793
PHAROS:  P19793
Entity Groups  
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UniProt GroupP19793
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gammaB [auth D]272Homo sapiensMutation(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
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UniProt GroupP37231
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 1, Co-activator PeptideC [auth B],
D [auth E]		12Homo sapiensMutation(s): 0 
Gene Names: NCOA1, BHLHE74, SRC1
EC: 2.3.1.48
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Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
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UniProt GroupQ15788
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D30
Query on D30
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
9RA
Query on 9RA
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding 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 = 179.258α = 90
b = 53.825β = 107.74
c = 67.108γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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