9RCG | pdb_00009rcg

Vitamin D receptor complex with a vitamin D receptor agonist/histone deacetylase inhibitor hybrid molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.206 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9RCG

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Hyperagonism of a Vitamin D Receptor Agonist/Histone Deacetylase Inhibitor Hybrid Molecule.

Sarmadi, F.Caza, A.Gao, Z.Rochel, N.Gleason, J.L.White, J.H.

(2025) J Med Chem 68: 20675-20688

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01932
  • Primary Citation Related Structures: 
    9RCG

  • PubMed Abstract: 

    1,25-Dihydroxyvitamin D (1,25D) analogs engage the vitamin D receptor (VDR) and can exert anticancer and immunomodulatory effects. Although tumors often resist 1,25D monotherapy, combining VDR agonism with histone deacetylase inhibitors (HDACi) restores anticancer efficacy. Here, we present AC-340, a novel bifunctional molecule that incorporates HDACi into a VDR agonist backbone. Besides its robust bifunctionality in vitro in multiple melanoma models, RNaseq analysis of B16-F10 mouse melanoma cells revealed that AC-340 superinduces the expression of a broad array of VDR target genes. Comparative structural studies and ChIP-qPCR revealed that AC-340 forms more interactions than 1,25D with residues in the VDR coactivator binding domain, leading to more efficacious recruitment of coactivator CBP. This, likely coupled with AC-340 HDACi activity, leads to elevated H3K27 acetylation of VDR target genes, a mark of active transcription. Thus, AC-340 functions as a VDR hyperagonist and should be efficacious in mono- or combination therapies against multiple cancer models.


  • Organizational Affiliation
    • Department of Physiology, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada.

Macromolecule Content 

  • Total Structure Weight: 36.12 kDa 
  • Atom Count: 2,226 
  • Modeled Residue Count: 251 
  • Deposited Residue Count: 315 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Vitamin D3 receptor A302Danio rerioMutation(s): 0 
Gene Names: vdranr1i1avdr
UniProt
Find proteins for Q9PTN2 (Danio rerio)
Explore Q9PTN2 
Go to UniProtKB:  Q9PTN2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9PTN2
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 213Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JD5
(Subject of Investigation/LOI)

Query on A1JD5



Download:Ideal Coordinates CCD File
C [auth A]4-[4-[3-[5-[(3~{S})-4,4-dimethyl-3-oxidanyl-pentyl]-4-methyl-1,3-thiazol-2-yl]pentan-3-yl]phenoxy]-~{N}-oxidanyl-butanamide
C26 H40 N2 O4 S
CHEHAHOVAVDOHQ-QFIPXVFZSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.206 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.02α = 90
b = 66.02β = 90
c = 262.51γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-10-01 
  • Deposition Author(s): Rochel, N.

Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release
  • Version 1.1: 2025-10-22
    Changes: Database references