5AWJ

Crystal structure of VDR-LBD/partial agonist complex: 22S-hexyl analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


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Literature

Fine tuning of agonistic/antagonistic activity for vitamin D receptor by 22-alkyl chain length of ligands: 22S-Hexyl compound unexpectedly restored agonistic activity.

Anami, Y.Sakamaki, Y.Itoh, T.Inaba, Y.Nakabayashi, M.Ikura, T.Ito, N.Yamamoto, K.

(2015) Bioorg.Med.Chem. 23: 7274-7281

  • DOI: 10.1016/j.bmc.2015.10.026
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 1α,25-Dihydroxyvitamin D3 exerts its actions by binding to vitamin D receptor (VDR). We are continuing the study related to the alteration of pocket structure of VDR by 22-alkyl substituent of ligands and the relationships between the alteration and ...

    1α,25-Dihydroxyvitamin D3 exerts its actions by binding to vitamin D receptor (VDR). We are continuing the study related to the alteration of pocket structure of VDR by 22-alkyl substituent of ligands and the relationships between the alteration and agonistic/antagonistic activity. Previously we reported that compounds 2 (22-H), 3 (22S-Et), and 4 (22S-Bu) are VDR agonist, partial agonist and antagonist, respectively. Here, we describe the synthesis and biological evaluation of 22S-hexyl analog 5 (22S-Hex), which was designed to be a stronger VDR antagonist than 4. Unexpectedly, 5 showed partial agonistic but not antagonistic activity when bound to VDR, indicating that it is not necessarily true that the bulkier the side chain is, the stronger the antagonistic activity will be. X-ray crystallographic analysis of the VDR-ligand-binding domain (VDR-LBD) accommodating compound 5 indicated that the partial agonist activity of 5 is dependent on the mixed population of the agonistic and antagonistic conformations. Binding of compound 5 may not bring the complex into the only antagonistic conformation due to the large conformational change of the VDR-LBD. From this study it was found that fine tuning of agonistic/antagonistic activity for VDR is possible by 22-alkyl chain length of ligands.


    Organizational Affiliation

    Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan. Electronic address: yamamoto@ac.shoyaku.ac.jp.,Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.,School of Biomedical Science, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan.,Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor,Vitamin D3 receptor
A
271Rattus norvegicusMutation(s): 0 
Gene Names: Vdr (Nr1i1)
Find proteins for P13053 (Rattus norvegicus)
Go to UniProtKB:  P13053
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 1
C
13Homo sapiensMutation(s): 0 
Gene Names: MED1 (ARC205, CRSP1, CRSP200, DRIP205, DRIP230, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2)
Find proteins for Q15648 (Homo sapiens)
Go to Gene View: MED1
Go to UniProtKB:  Q15648
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YSL
Query on YSL

Download SDF File 
Download CCD File 
A
(1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,3S)-3-(2-hydroxyethyl)nonan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol
C30 H50 O3
JUQILRKVRIIJNO-FJOOTJEJSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YSLIC50: 0.21 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 153.477α = 90.00
b = 43.447β = 100.53
c = 42.317γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-18
    Type: Initial release