8PWM

Crystal structure of VDR in complex with Des-C-Ring and Aromatic-D-Ring analog 3b

• PDB DOI: https://doi.org/10.2210/pdb8PWM/pdb

• Classification: TRANSCRIPTION
• Organism(s): Danio rerio, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-07-20 Released: 2024-08-21 
• Deposition Author(s): Rochel, N.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.252 
• R-Value Work: 0.196 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

Novel Des-C-Ring and Aromatic-D-Ring analogs Acting as Potent Agonists of the Vitamin D Receptor (VDR)

Rochel, N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 36.19 kDa 
• Atom Count: 2,106 
• Modelled Residue Count: 248 
• Deposited Residue Count: 315 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor A	A	302	Danio rerio	Mutation(s): 0  Gene Names: vdra, nr1i1a, vdr
UniProt
Find proteins for Q9PTN2 (Danio rerio) Explore Q9PTN2  Go to UniProtKB:  Q9PTN2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2	B	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
PHAROS:  Q15596 GTEx:  ENSG00000140396

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HXI (Subject of Investigation/LOI)	D [auth A]	(1R,3S,5Z)-4-methylidene-5-[(E)-3-[3-[7,7,7-tris(fluoranyl)-6-oxidanyl-6-(trifluoromethyl)hept-3-ynyl]phenyl]but-2-enylidene]cyclohexane-1,3-diol C25 H26 F6 O3 YPFOJCHONFJOGI-SGTALLODSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.252 
• R-Value Work: 0.196 
• R-Value Observed: 0.201 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.849	α = 90
b = 65.849	β = 90
c = 264.213	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-21 
Deposition Author(s): Rochel, N.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	--

Revision History  

• Version 1.0: 2024-08-21
  Type: Initial release