1K74

The 2.3 Angstrom resolution crystal structure of the heterodimer of the human PPARgamma and RXRalpha ligand binding domains respectively bound with GW409544 and 9-cis retinoic acid and co-activator peptides.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structural determinants of ligand binding selectivity between the peroxisome proliferator-activated receptors.

Xu, H.E., Lambert, M.H., Montana, V.G., Plunket, K.D., Moore, L.B., Collins, J.L., Oplinger, J.A., Kliewer, S.A., Gampe Jr., R.T., McKee, D.D., Moore, J.T., Willson, T.M.

(2001) Proc Natl Acad Sci U S A 98: 13919-13924

  • DOI: 10.1073/pnas.241410198
  • Primary Citation of Related Structures:  
    1K74, 1K7L

  • PubMed Abstract: 

    • The peroxisome proliferator-activated receptors (PPARs) are transcriptional regulators of glucose, lipid, and cholesterol metabolism. We report the x-ray crystal structure of the ligand binding domain of PPAR alpha (NR1C1) as a complex with the agonist ligand GW409544 and a coactivator motif from the steroid receptor coactivator 1 ...

    The peroxisome proliferator-activated receptors (PPARs) are transcriptional regulators of glucose, lipid, and cholesterol metabolism. We report the x-ray crystal structure of the ligand binding domain of PPAR alpha (NR1C1) as a complex with the agonist ligand GW409544 and a coactivator motif from the steroid receptor coactivator 1. Through comparison of the crystal structures of the ligand binding domains of the three human PPARs, we have identified molecular determinants of subtype selectivity. A single amino acid, which is tyrosine in PPAR alpha and histidine in PPAR gamma, imparts subtype selectivity for both thiazolidinedione and nonthiazolidinedione ligands. The availability of high-resolution cocrystal structures of the three PPAR subtypes will aid the design of drugs for the treatments of metabolic and cardiovascular diseases.

    Organizational Affiliation: 

    Nuclear Receptor Discovery Research, GlaxoSmithKline, Research Triangle Park, NC 27709, USA. ex11957@gsk.com



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alphaA238Homo sapiensMutation(s): 0 
Gene Names: RXRA, NR2B1
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
NIH Common Fund Data Resources
PHAROS:  P19793
GTEx:  ENSG00000186350
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator activated receptor gammaB [auth D]283Homo sapiensMutation(s): 0 
Gene Names: PPARG, NR1C3
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS:  P37231
GTEx:  ENSG00000132170
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
steroid receptor coactivatorC [auth B], D [auth E]25N/AMutation(s): 0 
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS:  Q15788
GTEx:  ENSG00000084676
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
544
Query on 544
Download Ideal Coordinates CCD File 
 F [auth D]2-(1-METHYL-3-OXO-3-PHENYL-PROPYLAMINO)-3-{4-[2-(5-METHYL-2-PHENYL-OXAZOL-4-YL)-ETHOXY]-PHENYL}-PROPIONIC ACID
C31 H30 N2 O5
GGUVRMBIEPYOKL-WMVCGJOFSA-N		 Ligand Interaction
9CR
Query on 9CR
Download Ideal Coordinates CCD File 
 E [auth A](9cis)-retinoic acid
C20 H28 O2
SHGAZHPCJJPHSC-ZVCIMWCZSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9CRIC50:  82   nM  BindingDB
9CREC50:  10   nM  BindingDB
9CRKd:  35   nM  BindingDB
9CREC50:  13   nM  BindingDB
9CREC50:  200   nM  BindingDB
9CRKi:  7.400000095367432   nM  BindingDB
9CRKd:  15   nM  BindingDB
9CRKi:  27   nM  BindingDB
9CRKi:  14   nM  BindingDB
9CREC50:  4.300000190734863   nM  BindingDB
9CRKd:  240   nM  BindingDB
9CRKi:  11   nM  BindingDB
9CRKd:  32   nM  BindingDB
9CRKi:  12   nM  BindingDB
9CRKi:  13   nM  BindingDB
9CRKi:  8   nM  BindingDB
9CRKi:  9   nM  BindingDB
9CREC50:  6   nM  BindingDB
9CRKd:  50   nM  BindingDB
9CRKd:  4   nM  BindingDB
9CRIC50:  32   nM  BindingDB
9CREC50:  195   nM  BindingDB
9CRIC50:  29   nM  BindingDB
9CREC50:  4.5   nM  BindingDB
9CRIC50:  12   nM  BindingDB
9CRKd:  30   nM  BindingDB
9CRKd:  1560   nM  BindingDB
9CRKd:  1810   nM  BindingDB
9CREC50:  250   nM  BindingDB
9CRKd:  8   nM  BindingDB
9CREC50:  29   nM  BindingDB
9CRKd:  9   nM  BindingDB
9CREC50:  316   nM  BindingDB
9CREC50:  2.5999999046325684   nM  BindingDB
9CRKi:  3.799999952316284   nM  BindingDB
9CREC50:  1.5   nM  BindingDB
9CRKi:  8.399999618530273   nM  BindingDB
9CRKd:  15   nM  BindingDB
9CRKd:  13   nM  BindingDB
9CRKd:  14   nM  BindingDB
9CRKd:  14   nM  BindingDB
9CRKd:  16   nM  BindingDB
9CRKd:  12   nM  BindingDB
9CRKd:  1.5   nM  BindingDB
9CRKd:  11   nM  BindingDB
544EC50:  0.2800000011920929   nM  BindingDB
9CREC50:  110   nM  BindingDB
9CREC50:  219   nM  BindingDB
9CREC50:  120   nM  BindingDB
9CRKd:  3   nM  BindingDB
9CREC50:  124   nM  BindingDB
9CREC50:  140   nM  BindingDB
9CREC50:  100   nM  BindingDB
9CREC50:  128   nM  BindingDB
9CREC50:  120   nM  BindingDB
9CREC50:  200   nM  BindingDB
9CRIC50:  4   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.62α = 90
b = 55.1β = 90
c = 214.86γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNXrefinement
MARdata reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-12-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-12-26
    Changes: Non-polymer description