9VOL | pdb_00009vol

Vitamin D receptor complex with a 4-{4-(m-carboran-1-yl)-2-methylphenoxy}butanoic acid derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Design, synthesis and structural development of nonsecosteroidal VDR ligands based on the C,C'-diphenyl-m-carborane scaffold.

Mudiyanselage, H.N.T.N.Misawa, T.Ochiai, K.Demizu, Y.Hanazono, Y.Ito, N.Fujii, S.

(2025) Eur J Med Chem 302: 118320-118320

  • DOI: https://doi.org/10.1016/j.ejmech.2025.118320
  • Primary Citation of Related Structures:  
    9VOG, 9VOH, 9VOI, 9VOJ, 9VOK, 9VOL

  • PubMed Abstract: 

    Nonsecosteroidal vitamin D receptor (VDR) ligands are promising drug candidates for multiple diseases, including osteoporosis, psoriasis, and certain cancers. We report here the design, synthesis, biological evaluation and crystallographic analysis of a series of 1,7-diphenyl-m-carborane derivatives as novel nonsecosteroidal VDR ligands. We found that the 1,7-diphenyl-m-carborane framework is a promising hydrophobic core of VDR ligands, and developed a series of potent compounds such as 12b and 13a. Interestingly, compounds with different chain length exhibited similar potencies. X-Ray co-crystal structure analysis revealed that the developed compounds exhibited various different interaction patterns depending on the structure of the carboxyalkyl chain, indicating that the ligand-binding pocket of the VDR possesses sufficient conformational plasticity to accommodate a wide variety of ligands without compromising activity. The developed carborane derivatives are promising leads for further structural development, and the findings on the diversity of binding modes will be helpful in the design of other VDR ligands.


  • Organizational Affiliation
    • Laboratory for Biomaterials and Bioengineering, Institute of Integrated Research, Institute of Science Tokyo, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan; Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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

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
A1MAU (Subject of Investigation/LOI)
Query on A1MAU

Download Ideal Coordinates CCD File 
C [auth A]4-[4-{7-(4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl)-1,7-dicarba-closo-dodecaboran-1-yl}-2-methylphenoxy]butyric acid
C22 H28 B10 F6 O4
ZOHWYNYTYWWWEN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.63α = 90
b = 41.6β = 96.236
c = 42.09γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release