3TKC

Design, Synthesis, Evaluation and Structure of Vitamin D Analogues with Furan Side Chains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Design, synthesis, evaluation, and structure of vitamin D analogues with furan side chains.

Fraga, R.Zacconi, F.Sussman, F.Ordonez-Moran, P.Munoz, A.Huet, T.Molnar, F.Moras, D.Rochel, N.Maestro, M.Mourino, A.

(2012) Chemistry 18: 603-612

  • DOI: 10.1002/chem.201102695

  • PubMed Abstract: 
  • Based on the crystal structures of human vitamin D receptor (hVDR) bound to 1α,25-dihydroxy-vitamin D(3) (1,25 D) and superagonist ligands, we previously designed new superagonist ligands with a tetrahydrofuran ring at the side chain that optimize th ...

    Based on the crystal structures of human vitamin D receptor (hVDR) bound to 1α,25-dihydroxy-vitamin D(3) (1,25 D) and superagonist ligands, we previously designed new superagonist ligands with a tetrahydrofuran ring at the side chain that optimize the aliphatic side-chain conformation through an entropy benefit. Following a similar strategy, four novel vitamin D analogues with aromatic furan side chains (3a, 3b, 4a, 4b) have now been developed. The triene system has been constructed by an efficient stereoselective intramolecular cyclization of an enol triflate (A-ring precursor) followed by a Suzuki-Miyaura coupling of the resulting intermediate with an alkenyl boronic ester (CD-side chain, upper fragment). The furan side chains have been constructed by gold chemistry. These analogues exhibit significant pro-differentiation effects and transactivation potency. The crystal structure of 3a in a complex with the ligand-binding domain of hVDR revealed that the side-chain furanic ring adopts two conformations.


    Organizational Affiliation

    Departamento de Química Orgánica, Universidad de Santiago y Unidad Asociada al CSIC, Avda de las Ciencias s/n, 15782 Santiago de Compostela, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor
A
259Homo sapiensMutation(s): 0 
Gene Names: VDR (NR1I1)
Find proteins for P11473 (Homo sapiens)
Go to Gene View: VDR
Go to UniProtKB:  P11473
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FMV
Query on FMV

Download SDF File 
Download CCD File 
A
(1S,3R,5Z,7E,14beta,17alpha,20S)-20-[5-(1-hydroxy-1-methylethyl)furan-2-yl]-9,10-secopregna-5,7,10-triene-1,3-diol
C28 H40 O4
LQSIVELXOQAADQ-YQCVTLPCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.018α = 90.00
b = 51.622β = 90.00
c = 132.818γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
HKL-2000data scaling
HKL-2000data reduction
MxCuBEdata collection
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-07
    Type: Initial release