7C7V

Vitamin D3 receptor/lithochoric acid derivative complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.198 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Lithocholic Acid Derivatives as Potent Vitamin D Receptor Agonists.

Sasaki, H.Masuno, H.Kawasaki, H.Yoshihara, A.Numoto, N.Ito, N.Ishida, H.Yamamoto, K.Hirata, N.Kanda, Y.Kawachi, E.Kagechika, H.Tanatani, A.

(2021) J Med Chem 64: 516-526

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01420
  • Primary Citation of Related Structures:  
    7C7V, 7C7W

  • PubMed Abstract: 

    Lithocholic acid ( 2 ) was identified as a second endogenous ligand of vitamin D receptor (VDR), though its activity is very weak. In this study, we designed novel lithocholic acid derivatives based on the crystal structure of VDR-ligand-binding domain (LBD) bound to 2 . Among the synthesized compounds, 6 bearing a 2-hydroxy-2-methylprop-1-yl group instead of the 3-hydroxy group at the 3α-position of 2 showed dramatically increased activity in HL-60 cell differentiation assay, being at least 10 000 times more potent than lithocholic acid ( 2 ) and 3 times more potent than 1α,25-dihydroxyvitamin D 3 ( 1 ). Although the binding affinities of 6 and its epimer 7 were less than that of 1 , their transactivation activities were greater than that of 1 . X-ray structure analyses of VDR LBD bound to 6 or 7 showed that the binding positions of these compounds in the ligand-binding pocket are similar to that of 1 .


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vitamin D3 receptor271Rattus norvegicusMutation(s): 0 
Gene Names: VdrNr1i1
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

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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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FKC (Subject of Investigation/LOI)
Query on FKC

Download Ideal Coordinates CCD File 
C [auth A](4R)-4-[(3R,5R,8R,9S,10S,13R,14S,17R)-10,13-dimethyl-3-(2-methyl-2-oxidanyl-propyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]pentanoic acid
C28 H48 O3
YEJWIEPCSOSHIJ-CUYCEIPOSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
D [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.045α = 90
b = 36.898β = 96.963
c = 39.486γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description