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


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:  
    3H0A, 3GZ9

  • 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alphaA228Homo sapiensMutation(s): 0 
Gene Names: RXRANR2B1
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
NIH Common Fund Data Resources
PHAROS:  P19793
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gammaB [auth D]272Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS:  P37231
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 1, Co-activator PeptideC [auth B], D [auth E]12Homo sapiensMutation(s): 0 
Gene Names: NCOA1BHLHE74SRC1
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS:  Q15788
Protein Feature View
Expand
  • 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9RAKi:  36   nM  BindingDB
D30EC50:  160   nM  BindingDB
9RAEC50:  25   nM  BindingDB
9RAKd:  36   nM  BindingDB
9RAKd:  42   nM  BindingDB
9RAKi:  21   nM  BindingDB
9RAKd:  21   nM  BindingDB
9RAEC50:  149   nM  BindingDB
9RAKd:  51   nM  BindingDB
9RAKi:  21   nM  BindingDB
9RAEC50:  118   nM  BindingDB
9RAEC50:  20   nM  BindingDB
9RAEC50:  19.799999237060547   nM  BindingDB
9RAKi:  29   nM  BindingDB
9RAKi:  21   nM  BindingDB
9RAEC50:  52   nM  BindingDB
9RAKd:  29   nM  BindingDB
9RAKd:  18   nM  BindingDB
9RAEC50:  40   nM  BindingDB
D30Ki:  33   nM  BindingDB
9RAEC50:  42   nM  BindingDB
9RAEC50:  122   nM  BindingDB
9RAKd:  26   nM  BindingDB
9RAKi:  75   nM  BindingDB
9RAKd:  28   nM  BindingDB
9RAEC50:  112   nM  BindingDB
9RAEC50:  40   nM  BindingDB
9RAEC50:  20   nM  BindingDB
D30Ki :  33   nM  PDBBind
9RAKi:  29   nM  BindingDB
9RAEC50:  32   nM  BindingDB
9RAEC50:  33   nM  BindingDB
9RAKi:  14   nM  BindingDB
9RAEC50:  2.700000047683716   nM  BindingDB
9RAEC50:  28   nM  BindingDB
D30Ki:  33   nM  Binding MOAD
9RAKd:  14   nM  BindingDB
9RAKi:  16   nM  BindingDB
9RAKi:  5.900000095367432   nM  BindingDB
9RAKd:  1590   nM  BindingDB
9RAEC50:  20   nM  BindingDB
9RAKi:  8.300000190734863   nM  BindingDB
9RAKd:  1890   nM  BindingDB
9RAEC50:  24   nM  BindingDB
9RAEC50:  25   nM  BindingDB
9RAEC50:  25   nM  BindingDB
9RAEC50:  24   nM  BindingDB
9RAKd:  7   nM  BindingDB
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

View Full Validation Report



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