7B39 | pdb_00007b39

Allene-Based Design of a Noncalcemic Vitamin D Receptor Agonist

• PDB DOI: https://doi.org/10.2210/pdb7B39/pdb

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


• Deposited: 2020-11-29 Released: 2021-09-01 
• Deposition Author(s): Rochel, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Design, Synthesis, Evaluation and Structure of Allenic 1 alpha ,25-Dihydroxyvitamin D 3 Analogs with Locked Mobility at C-17.

Fraga, R., Len, K., Lutzing, R., Laverny, G., Loureiro, J., Maestro, M.A., Rochel, N., Rodriguez-Borges, E., Mourino, A.

(2021) Chemistry 27: 13384-13389

• PubMed: 34224173 
• DOI: https://doi.org/10.1002/chem.202101578
• Primary Citation Related Structures: 
  7B39


• PubMed Abstract: 
  

  Vitamin D receptor ligands have potential for the treatment of hyperproliferative diseases and disorders related to the immune system. However, hypercalcemic effects limit their therapeutical uses and call for the development of tissue-selective new analogs. We have designed and synthesized the first examples of 1α,25-dihydroxyvitamin D ₃ analogs bearing an allenic unit attached to the D ring to restrict the side-chain conformational mobility. The triene system was constructed by a Pd ⁰ -mediated cyclization/Suzuki-Miyaura cross-coupling process in the presence of an allenic side chain. The allenic moiety was built through an orthoester-Claisen rearrangement of a propargylic alcohol. The biological activity and structure of (22S)-1α,25-dihydroxy-17,20-dien-24-homo-21-nor-vitamin D ₃ bound to binding domain of the vitamin D receptor, provide information concerning side-chain conformational requirements for biological activity.

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Organizational Affiliation: 
• Departamento de Química Orgánica, Laboratorio de Investigación Ignacio Ribas, Universidad de Santiago, Avda Ciencias s/n, 15782, Santiago de Compostela, Spain.
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.
LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Portugal.
Departamento de Química-CICA, Facultad de Ciencias, Universidad de A Coruña, Campus da Zapateira s/n, 15071, A Coruña, Spain.

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: 36.31 kDa 
• Atom Count: 2,156 
• Modeled Residue Count: 251 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T0H (Subject of Investigation/LOI)	C [auth A]	(1R,3S,Z)-5-(2-((3aS,7aS,E)-1-(6-hydroxy-6-methylhept-1-en-1-ylidene)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-4-methylenecyclohexane-1,3-diol C27 H40 O3 ZUEJBGWNHJHNIO-PIOXGFLRSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.25	α = 90
b = 66.25	β = 90
c = 264.39	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	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: 2021-09-29
  Changes: Data collection, Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description