7OXZ | pdb_00007oxz

VDR complex with a side-chain hydroxylated derivative of lithocholic acid

• PDB DOI: https://doi.org/10.2210/pdb7OXZ/pdb

• Classification: TRANSCRIPTION
• Organism(s): Danio rerio, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-06-23 Released: 2021-09-01 
• Deposition Author(s): Rochel, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.254 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis and evaluation of side-chain hydroxylated derivatives of lithocholic acid as potent agonists of the vitamin D receptor (VDR).

Gonzalez, C.M., Gaikwad, S., Lasanta, G., Loureiro, J., Nilsson, N., Peluso-Iltis, C., Rochel, N., Mourino, A.

(2021) Bioorg Chem 115: 105202-105202

• PubMed: 34339974 
• DOI: https://doi.org/10.1016/j.bioorg.2021.105202
• Primary Citation Related Structures: 
  7OXZ, 7OY4


• PubMed Abstract: 
  

  A high number of biologically active and low-calcemic secosteroidal ligands of the vitamin D receptor (VDR) have been developed, some of which are already used clinically although with limited success in the treatment of hyperproliferative diseases because the required pharmaceutical dosages induce toxicity. We describe here the in silico design, synthesis, structural analysis and biological evaluation of two novel active lithocholic acid derivatives hydroxylated at the side chain as highly potent inhibitors of atopic dermatitis-relevant keratinocyte inflammation of potential therapeutic interest.

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Organizational Affiliation: 
• Departamento de Química Orgánica, Laboratorio de Investigación Ignacio Ribas, Universidad de Santiago de Compostela, Avda das Ciencias s/n, 15782 Santiago de Compostela, Spain.
LEO Pharma, Open Innovation, Industriparken 55, 2750 Ballerup, Denmark.
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; Institut National de La Santé et de La Recherche Médicale (INSERM), U1258, 67400 Illkirch, France; Centre National de Recherche Scientifique (CNRS), UMR7104, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France.
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; Institut National de La Santé et de La Recherche Médicale (INSERM), U1258, 67400 Illkirch, France; Centre National de Recherche Scientifique (CNRS), UMR7104, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France. Electronic address: [e-mail].
Departamento de Química Orgánica, Laboratorio de Investigación Ignacio Ribas, Universidad de Santiago de Compostela, Avda das Ciencias s/n, 15782 Santiago de Compostela, Spain. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.3 kDa 
• Atom Count: 2,071 
• Modeled Residue Count: 247 
• Deposited Residue Count: 317 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor A	A	302	Danio rerio	Mutation(s): 0  Gene Names: vdra, nr1i1a, vdr
UniProt
Find proteins for Q9PTN2 (Danio rerio) Explore Q9PTN2  Go to UniProtKB:  Q9PTN2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1	B	15	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2UI (Subject of Investigation/LOI)	C [auth A]	(3R,6R)-6-[(3R,5R,8R,9S,10S,13R,14S,17R)-10,13-dimethyl-3-(2-methyl-2-oxidanyl-propyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]heptane-1,3-diol C30 H54 O3 BELGEHMGZKEZEK-JSCSUZHRSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.254 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.38	α = 90
b = 66.38	β = 90
c = 263.186	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
STARANISO	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-01 
Deposition Author(s): Rochel, N.

Revision History  

• Version 1.0: 2021-09-01
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description