4ITE

Crystal structure of the human vitamin D receptor ligand binding domain complexed with 1alpha,25-Dihydroxy-2alpha-[2-(2H-tetrazol-2-yl)ethyl]vitamin D3

• PDB DOI: https://doi.org/10.2210/pdb4ITE/pdb

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


• Deposited: 2013-01-18 Released: 2014-01-22 
• Deposition Author(s): Kakuda, S., Takimoto-Kamimura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Synthesis of 2 alpha-heteroarylalkyl active vitamin d3 with therapeutic effect on enhancing bone mineral density in vivo

Matsuo, M., Hasegawa, A., Takano, M., Saito, H., Kakuda, S., Chida, T., Takagi, K., Ochiai, E., Horie, K., Harada, Y., Takimoto-Kamimura, M., Takenouchi, K., Sawada, D., Kittaka, A.

(2013) ACS Med Chem Lett 4: 671-674

• PubMed: 24900728 
• DOI: https://doi.org/10.1021/ml400098w
• Primary Citation of Related Structures:  
  4ITE, 4ITF


• PubMed Abstract: 
  

  2α-Heteroarylethyl-1α,25-dihydroxyvitamin D3 analogues, which were designed to form a hydrogen bond between Arg274 of human vitamin D receptor (hVDR) and a nitrogen atom of the heteroaromatic ring at the 2α-position, were synthesized. Among them, 2α-[2-(tetrazol-2-yl)ethyl]-1α,25-dihydroxyvitamin D3 showed higher osteocalcin promoter transactivation activity in human osteosarcoma (HOS) cells and a greater therapeutic effect in ovariectomized (OVX) rats, osteoporosis model animals, on enhancing bone mineral density than those of active vitamin D3. X-ray cocrystallographic analysis of the hVDR-ligand complex confirms that the new hydrogen bond formation stabilized the complex.

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Organizational Affiliation: 

Faculty of Pharmaceutical Sciences, Teikyo University , Itabashi-ku, Tokyo 173-8605, 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: 30.32 kDa 
• Atom Count: 2,103 
• 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
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
TEY	B [auth A]	(1R,2S,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-2-[2-(1,2,3,4-tetrazol-2-yl)ethyl]cyclohexane-1,3-diol C30 H48 N4 O3 IFHRQILUGOUOIV-YVUZACRZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.76	α = 90
b = 51.531	β = 90
c = 131.781	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: 2014-01-22 
Deposition Author(s): Kakuda, S., Takimoto-Kamimura, M.

Revision History  

• Version 1.0: 2014-01-22
  Type: Initial release
  
• Version 1.1: 2014-08-13
  Changes: Database references
• Version 1.2: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description