Download MendeleyNovel Des-C-Ring and Aromatic-D-Ring analogs Acting as Potent Agonists of the Vitamin D Receptor (VDR)
Rochel, N.To be published.
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
- Funding Organization(s): Agence Nationale de la Recherche (ANR)
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
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This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Vitamin D3 receptor 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 Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9PTN2 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Nuclear receptor coactivator 2 | 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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q15596 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HXI (Subject of Investigation/LOI) Query on HXI | 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 Query on 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 Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-08-21 Deposition Author(s): Rochel, N.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Agence Nationale de la Recherche (ANR) | France | -- |
Revision History (Full details and data files)
- Version 1.0: 2024-08-21
Type: Initial release
