3P8X

Synthesis, Structure, and Biological Activity of des-Side Chain Analogues of 1alpha,25-Dihydroxyvitamin D3 with Substituents at C-18

• PDB DOI: https://doi.org/10.2210/pdb3P8X/pdb

• Classification: Transcription Regulator
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-10-15 Released: 2011-08-31 
• Deposition Author(s): Rochel, N., Sato, Y., Moras, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Synthesis, Structure, and Biological Activity of des-Side Chain Analogues of 1 ,25-Dihydroxyvitamin D3 with Substituents at C-18

Verlinden, L., Verstuyf, A., Eelen, G., Bouillon, R., Ordonez-Moran, P., Larriba, M.J., Munoz, A., Rochel, N., Sato, Y., Moras, D., Maestro, M., Seoane, S., Dominguez, F., Eduardo-Canosa, S., Nicoletti, D., Moman, E., Mourino, A.

(2011) ChemMedChem 6: 788-793

• PubMed: 21520419 
• DOI: https://doi.org/10.1002/cmdc.201100021
• Primary Citation of Related Structures:  
  3P8X


• PubMed Abstract: 
  

  An improved synthetic route to 1α,25-dihydroxyvitamin D(3) des-side chain analogues 2 a and 2 b with substituents at C18 is reported, along with their biological activity. These analogues display significant antiproliferative effects toward MCF-7 breast cancer cells and prodifferentiation activity toward SW480-ADH colon cancer cells; they are also characterized by a greatly decreased calcemic profile. The crystal structure of the human vitamin D receptor (hVDR) complexed to one of these analogues, 20(17→18)-abeo-1α,25-dihydroxy-22-homo-21-norvitamin D(3) (2 a) reveals that the side chain introduced at position C18 adopts the same orientation in the ligand binding pocket as the side chain of 1α,25-dihydroxyvitamin D(3).

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Organizational Affiliation: 

Laboratorium voor Experimentele Geneeskunde en Endocrinologie, Katholieke Universiteit Leuven, Leuven, Belgium.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 32.3 kDa 
• Atom Count: 2,304 
• Modelled Residue Count: 255 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor	A	280	Homo sapiens	Mutation(s): 0  Gene Names: VDR, NR1I1
UniProt & NIH Common Fund Data Resources
Find proteins for P11473 (Homo sapiens) Explore P11473  Go to UniProtKB:  P11473
PHAROS:  P11473 GTEx:  ENSG00000111424

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZYD	B [auth A]	(1R,3S,5Z)-5-{(2E)-2-[(3aR,7aS)-7a-(7-hydroxy-7-methyloctyl)octahydro-4H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol C27 H44 O3 FJGYNKGWOKETAA-AXVRRUDCSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.628	α = 90
b = 51.342	β = 90
c = 130.82	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Rochel, N., Sato, Y., Moras, D.

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2017-07-26
  Changes: Advisory, Refinement description, Source and taxonomy
• Version 1.2: 2024-02-21
  Changes: Advisory, Data collection, Database references, Derived calculations