9FW8 | pdb_00009fw8

VDR complex with UG-650

PDB DOI: https://doi.org/10.2210/pdb9FW8/pdb

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

Deposited: 2024-06-28 Released: 2025-05-07
Deposition Author(s): Rochel, N.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 ?
R-Value Free:
0.261 (Depositor), 0.256 (DCC)
R-Value Work:
0.198 (Depositor), 0.207 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Design, synthesis and biological evaluation of a novel non-Gemini analog of UVB1 and crystal structure of its complex with the vitamin D receptor.

Gomez-Bouzo, U., Peluso-Iltis, C., Santalla, H., Verlinden, L., Verstuyf, A., Rochel, N., Gomez, G., Fall, Y.

(2025) Bioorg Chem 157: 108239-108239

PubMed: 39938446 Search on PubMed
DOI: https://doi.org/10.1016/j.bioorg.2025.108239
Primary Citation of Related Structures:
9FW8

PubMed Abstract:
We synthesized UG-650, a novel non-Gemini analog of UVB1 that combines structural features of UVB1 and MC 1288. The evaluation of the bioactivities indicates that UG-650 dose-dependently inhibited MCF-7 cell proliferation. In comparison to calcitriol, slightly lower concentrations of UG-650 were needed to achieve equivalent levels of proliferation inhibition. Structural analysis revealed that the analog forms additional interactions stabilizing VDR active form.

Organizational Affiliation

Departamento de Química Orgánica and Instituto de Investigación Sanitaria Galicia Sur (IISGS), Campus Lagoas Marcosende, Universidad de Vigo 36310 Vigo, Spain.

Macromolecule Content

Total Structure Weight: 36.08 kDa
Atom Count: 2,115
Modelled Residue Count: 249
Deposited Residue Count: 315
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9PTN2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15596
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IGV (Subject of Investigation/LOI) Query on A1IGV Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(2~{S})-7-methyl-4-methylidene-7-oxidanyl-octan-2-yl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol C₂₉ H₄₆ O₃ LVXRHQNFZLEICU-LIOGGTHJSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]