7VQP | pdb_00007vqp

Vitamin D receptor complexed with a lithocholic acid derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 
    0.242 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.207 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Lithocholic Acid Amides as Potent Vitamin D Receptor Agonists.

Yoshihara, A.Kawasaki, H.Masuno, H.Takada, K.Numoto, N.Ito, N.Hirata, N.Kanda, Y.Ishizawa, M.Makishima, M.Kagechika, H.Tanatani, A.

(2022) Biomolecules 12

  • DOI: https://doi.org/10.3390/biom12010130
  • Primary Citation Related Structures: 
    7VQP

  • PubMed Abstract: 

    1α,25-Dihydroxyvitamin D 3 [1α,25(OH) 2 D 3 , 1 ] is an active form of vitamin D 3 and regulates various biological phenomena, including calcium and phosphate homeostasis, bone metabolism, and immune response via binding to and activation of vitamin D receptor (VDR). Lithocholic acid (LCA, 2 ) was identified as a second endogenous agonist of VDR, though its potency is very low. However, the lithocholic acid derivative 3 ( Dcha-20 ) is a more potent agonist than 1α,25(OH) 2 D 3 , ( 1 ), and its carboxyl group has similar interactions to the 1,3-dihydroxyl groups of 1 with amino acid residues in the VDR ligand-binding pocket. Here, we designed and synthesized amide derivatives of 3 in order to clarify the role of the carboxyl group. The synthesized amide derivatives showed HL-60 cell differentiation-inducing activity with potency that depended upon the substituent on the amide nitrogen atom. Among them, the N -cyanoamide 6 is more active than either 1 or 3 .


  • Organizational Affiliation
    • Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan.

Macromolecule Content 

  • Total Structure Weight: 32.67 kDa 
  • Atom Count: 1,981 
  • Modeled Residue Count: 241 
  • Deposited Residue Count: 284 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Vitamin D3 receptor271Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P13053 (Rattus norvegicus)
Explore P13053 
Go to UniProtKB:  P13053
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13053
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 1B [auth C]13Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15648 (Homo sapiens)
Explore Q15648 
Go to UniProtKB:  Q15648
PHAROS:  Q15648
GTEx:  ENSG00000125686 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15648
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7SW
(Subject of Investigation/LOI)

Query on 7SW



Download:Ideal Coordinates CCD File
C [auth A]3-((R)-4-((3R,5R,8R,9S,10S,13R,14S,17R)-3-(2-hydroxy-2-methylpropyl)-10,13-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-17-yl)pentanamido)propanoic acid
C31 H53 N O4
ZDSAGRUYIZLIJR-XARXUAFMSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free:  0.242 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.207 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.805α = 90
b = 37.581β = 98.59
c = 40.913γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Derived calculations, Refinement description