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 1RDT | pdb_00001rdt

Crystal Structure of a new rexinoid bound to the RXRalpha ligand binding doamin in the RXRalpha/PPARgamma heterodimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.259 (Depositor) 
  • R-Value Work: 
    0.221 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1RDT

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

Literature

Structure-based design of potent retinoid X receptor alpha agonists.

Haffner, C.D., Lenhard, J.M., Miller, A.B., McDougald, D.L., Dwornik, K., Ittoop, O.R., Gampe Jr., R.T., Xu, H.E., Blanchard, S., Montana, V.G., Consler, T.G., Bledsoe, R.K., Ayscue, A., Croom, D.

(2004) J Med Chem 47: 2010-2029

  • DOI: https://doi.org/10.1021/jm030565g
  • Primary Citation Related Structures: 
    1RDT

  • PubMed Abstract: 

    A series of tetrahydrobenzofuranyl and tetrahydrobenzothienyl propenoic acids that showed potent agonist activity against RXRalpha were synthesized via a structure-based design approach. Among the compounds studied, 46a,b showed not only very good potency against RXRalpha (K(i) = 6 nM) but was also found to be greater than 167-fold selective vs RARalpha (K(i) > 1000 nM). This compound profiled out as a full agonist in a cell-based transient transfection assay (EC(50) = 3 nM). The two antipodes were separated via chiral chromatography, and 46b was found to be 40-fold more potent than 46a. Interestingly, cocrystallization of 46a,b with the RXRalpha protein generated a liganded structure whereby the (S)-antipode was found in the binding pocket. Given orally in db/db mice or ZDF rats, 46a,b showed a significant glucose-lowering effect and an increase in liver mass. Triglycerides decreased significantly in db/db mice but increased in the ZDF rats. A dose-dependent decrease of nonesterified free fatty acids was seen in ZDF rats but not in db/db mice. These differences indicate a species specific effect of RXR agonists on lipid metabolism.


  • Organizational Affiliation: 
    • GlaxoSmithKline Research and Development, 5 Moore Drive, P.O. Box 13398, Research Triangle Park, NC 27709, USA. curt.d.haffner@gsk.com

Macromolecule Content 

  • Total Structure Weight: 65.77 kDa 
  • Atom Count: 4,027 
  • Modeled Residue Count: 480 
  • Deposited Residue Count: 574 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alpha242Homo sapiensMutation(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
GTEx:  ENSG00000186350 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19793
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
LxxLL motif coactivator25Homo sapiensMutation(s): 0 
Gene Names: NCOA1
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
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UniProt GroupQ15788
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Peroxisome proliferator activated receptor gammaC [auth D]284Homo 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
GTEx:  ENSG00000132170 
Entity Groups
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UniProt GroupP37231
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
LxxLL motif coactivatorD [auth E]23Homo sapiensMutation(s): 0 
Gene Names: CREBBP
EC: 2.3.1 (UniProt), 2.3.1.48 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92793 (Homo sapiens)
Explore Q92793 
Go to UniProtKB:  Q92793
PHAROS:  Q92793
GTEx:  ENSG00000005339 
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UniProt GroupQ92793
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
570

Query on 570



Download:Ideal Coordinates CCD File
F [auth D]2-(2-BENZOYL-PHENYLAMINO)-3-{4-[2-(5-METHYL-2-PHENYL-OXAZOL-4-YL)-ETHOXY]-PHENYL}-PROPIONIC ACID
C34 H30 N2 O5
ZZCHHVUQYRMYLW-HKBQPEDESA-N
L79

Query on L79



Download:Ideal Coordinates CCD File
E [auth A](S)-(2E)-3[4-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRO-2-NAPHTHALENYL)TETRAHYDRO-1-BENZOFURAN-2-YL]-2-PROPENOIC ACID
C25 H30 O3
WFLQBFXZEVUXMT-UEOKTHRPSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.259 (Depositor) 
  • R-Value Work:  0.221 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.69α = 90
b = 54.58β = 90
c = 211.7γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
CNXrefinement
HKL-2000data scaling
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary