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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alpha228Homo sapiensMutation(s): 0 
Gene Names: RXRANR2B1
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
PHAROS:  P19793
GTEx:  ENSG00000186350 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19793
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gammaB [auth D]272Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
PHAROS:  P37231
GTEx:  ENSG00000132170 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 1, Co-activator PeptideC [auth B],
D [auth E]
12Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000084676 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15788
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / 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
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
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 PDBBind:  3H0A Ki: 33 (nM) from 1 assay(s)
Binding MOAD:  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 


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
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations