3AX8

Crystal structure of the human vitamin D receptor ligand binding domain complexed with 15alpha-methoxy-1alpha,25-dihydroxyvitamin D3

• PDB DOI: https://doi.org/10.2210/pdb3AX8/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-30 Released: 2011-10-05 
• Deposition Author(s): Kakuda, S., Takimoto-Kamimura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.294 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 

Starting Model: experimental

Literature

New C15-substituted active vitamin D3

Shindo, K., Kumagai, G., Takano, M., Sawada, D., Saito, N., Saito, H., Kakuda, S., Takagi, K., Ochiai, E., Horie, K., Takimoto-Kamimura, M., Ishizuka, S., Takenouchi, K., Kittaka, A.

(2011) Org Lett 13: 2852-2855

• PubMed: 21539305 
• DOI: https://doi.org/10.1021/ol200828s
• Primary Citation of Related Structures:  
  3AX8


• PubMed Abstract: 
  

  C15-Substituted 1α,25-dihydroxyvitamin D(3) analogs were synthesized for the first time to investigate the effects of the modified CD-ring on biological activity concerning the agonistic positioning of helix-3 and helix-12 of the vitamin D receptor (VDR). X-ray cocrystallographic analysis proved that 0.6 Å shifts of the CD-ring and shrinking of the side chain were necessary to maintain the position of the 25-hydroxy group for proper interaction with helix-12. The 15-hydroxy-16-ene derivative showed higher binding affinity for hVDR than the natural hormone.

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Organizational Affiliation: 

Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa, Japan.

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: 30.25 kDa 
• Atom Count: 2,059 
• Modelled Residue Count: 253 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor	A	263	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EIM	B [auth A]	(1R,3S,5Z)-5-[(2E)-2-[(1R,3S,3aS,7aR)-1-[(2R)-6-hydroxy-6-methyl-heptan-2-yl]-3-methoxy-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol C28 H46 O4 MKYCMLKYANTZFR-GSVKQXOCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.294 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.489	α = 90
b = 51.585	β = 90
c = 132.017	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-05 
Deposition Author(s): Kakuda, S., Takimoto-Kamimura, M.

Revision History  

• Version 1.0: 2011-10-05
  Type: Initial release
  
• Version 1.1: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description