5OWD

Vitamin D receptor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.151 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Investigation of 20S-hydroxyvitamin D3 analogs and their 1 alpha-OH derivatives as potent vitamin D receptor agonists with anti-inflammatory activities.

Lin, Z.Marepally, S.R.Goh, E.S.Y.Cheng, C.Y.S.Janjetovic, Z.Kim, T.K.Miller, D.D.Postlethwaite, A.E.Slominski, A.T.Tuckey, R.C.Peluso-Iltis, C.Rochel, N.Li, W.

(2018) Sci Rep 8: 1478-1478

  • DOI: 10.1038/s41598-018-19183-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 20S-hydroxyvitamin D <sub>3 </sub> [20S(OH)D <sub>3 </sub>] is anti-inflammatory and not hypercalcemic, suggesting its potential as a lead compound. In this study, side chain modified 20S(OH)D <sub>3 </sub> analogs (4, 13, 23 and 33) together with th ...

    20S-hydroxyvitamin D 3 [20S(OH)D 3 ] is anti-inflammatory and not hypercalcemic, suggesting its potential as a lead compound. In this study, side chain modified 20S(OH)D 3 analogs (4, 13, 23 and 33) together with their 1α-OH derivatives were synthesized and their metabolism and biological activities tested. 4, 13 and 23 are good substrates for CYP27B1, enabling enzymatic synthesis of their 1α-OH derivatives 5, 14 and 24. However, 33 could not be hydroxylated by CYP27B1 and acts as an inhibitor. All analogs were poorer substrates for CYP24A1 than calcitriol, indicating improved catabolic stability. While the parent analogs showed minimal VDR stimulating activity, their 1α-OH derivatives were potent VDR agonists. 4, 5, 14 and 24 significantly upregulated the expression of CYP24A1 at the mRNA level, consistent with their VDR activation abilities and indicating that 1α-hydroxylation is required to produce analogs with strong activity. These analogs have anti-inflammatory activities that are influenced by side chain composition and by 1α-hydroxylation. To understand their molecular interactions with the VDR, 20S(OH)D 3 , 4 and 33 were co-crystalized with the VDR ligand binding domain, which revealed subtle differences to the calcitriol-bound receptor. This study demonstrates the potential of the 20S(OH)D 3 scaffold for the development of novel anti-inflammatory agents.


    Organizational Affiliation

    School of Molecular Sciences, University of Western Australia, Perth, WA, 6009, Australia.,Department of Dermatology, Comprehensive Cancer Center, Cancer Chemoprevention Program, University of Alabama at Birmingham, Birmingham, AL, 35294, United States.,Department of Integrative Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Centre National de la Recherche Scientifique, Institut National de la Santé de la Recherche Médicale, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, 67404, France.,Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, United States.,Pathology and Laboratory Medicine Service, VA Medical Center at Birmingham, Birmingham, AL, 35294, United States.,Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, United States. wli@uthsc.edu.,Department of Integrative Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Centre National de la Recherche Scientifique, Institut National de la Santé de la Recherche Médicale, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, 67404, France. rochel@igbmc.fr.,Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, United States.,Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163, United States.,Department of Veterans Affairs Medical Center, Memphis, TN, 38104, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor A
A
302Danio rerioMutation(s): 0 
Gene Names: vdra (nr1i1a, vdr)
Find proteins for Q9PTN2 (Danio rerio)
Go to UniProtKB:  Q9PTN2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 1
B
15Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B0B
Query on B0B

Download SDF File 
Download CCD File 
A
(1~{S},3~{Z})-3-[(2~{E})-2-[(1~{S},3~{a}~{S},7~{a}~{S})-7~{a}-methyl-1-[(2~{S})-6-methyl-2-oxidanyl-hept-5-en-2-yl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexan-1-ol
C27 H42 O2
LZELNYSXHKHQKY-LBRHRNEPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.151 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.206 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 65.750α = 90.00
b = 65.750β = 90.00
c = 262.970γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-08-31 
  • Released Date: 2018-02-07 
  • Deposition Author(s): Rochel, N., Li, W.

Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-13-BSV8-0024-01

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release