5XPL

Crystal structure of VDR-LBD complexed with 22S-butyl-25-hydroxyphenyl-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action

Kato, A.Yamao, M.Hashihara, Y.Ishida, H.Itoh, T.Yamamoto, K.

(2017) J. Med. Chem. 60: 8394-8406

  • DOI: 10.1021/acs.jmedchem.7b00819
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Vitamin D receptor (VDR) antagonists can be classified into two categories: the first category of VDR antagonists, which do not stabilize the helix 11-12, and the second category of antagonists, which destabilize the helix 6-7 region. To elucidate th ...

    Vitamin D receptor (VDR) antagonists can be classified into two categories: the first category of VDR antagonists, which do not stabilize the helix 11-12, and the second category of antagonists, which destabilize the helix 6-7 region. To elucidate the mechanism underlying the first category antagonists by using the crystal structure, we designed and synthesized several VDR ligands with a p-hydroxyphenyl group at the C25-position. Of these, 22S-butyl-25-carbonyl analogue 5b and 25-di-p-hydoroxyphenyl analogues 6a,b showed strong antagonistic activity. We succeeded in cocrystallizing the ligand-binding domain of VDR complexed with 5b and found that the structure showed an alternative conformation of the helix 11-12 that explained the mechanism of the first category antagonists. Taking the present and previous studies together, we could elucidate the mechanisms underlying first and second categories antagonists based on individual crystal structures. This study provides significant insights into antagonism against not only VDR but also nuclear receptors.


    Organizational Affiliation

    Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University , 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
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
Nuclear receptor coactivator 2
C
13Homo sapiensMutation(s): 0 
Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8C9
Query on 8C9

Download SDF File 
Download CCD File 
A
(4~{S})-4-[(1~{R})-1-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]ethyl]-1-(4-hydroxyphenyl)octan-1-one
22S-butyl-25-hydroxyphenyl-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3
C35 H50 O4
IDKWEPILMVJEEL-HXCBKPQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 128.780α = 90.00
b = 44.910β = 93.62
c = 45.520γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-06-13
    Type: Data collection, Database references