5XZF image
Entry Detail
PDB ID:
5XZF
Keywords:
Title:
Vitamin D receptor with a synthetic ligand ADRO1
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2017-07-12
Release Date:
2018-07-25
Method Details:
Experimental Method:
Resolution:
2.10 Å
R-Value Free:
0.21
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Vitamin D3 receptor
Mutations:165-211 deletion
Chain IDs:A
Chain Length:271
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Description:Mediator of RNA polymerase II transcription subunit 1
Chain IDs:B (auth: C)
Chain Length:13
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
25 S-Adamantyl-23-yne-26,27-dinor-1 alpha ,25-dihydroxyvitamin D3: Synthesis, Tissue Selective Biological Activities, and X-ray Crystal Structural Analysis of Its Vitamin D Receptor Complex.
J. Med. Chem. 61 6658 6673 (2018)
PMID: 29989817 DOI: 10.1021/acs.jmedchem.8b00427

Abstact

Both 25 R- and 25 S-25-adamantyl-23-yne-26,27-dinor-1α,25-dihydroxyvitamin D3 (4a and 4b) were stereoselectively synthesized by a Pd(0)-catalyzed ring closure and Suzuki-Miyaura coupling between enol-triflate 7 and alkenyl-boronic ester 8. The 25 S isomer (4b) showed high vitamin D receptor (VDR) affinity (50% of that of the natural hormone 1α,25-dihydroxyvitamin D3, 1) and transactivation potency (kidney HEK293, 90%). In endogenous gene expression, it showed high cell-type selectivity for kidney cells (HEK293, CYP24A1 160% of 1), bone cells (MG63, osteocalcin 64%), and monocytes (U937, CAMP 96%) over intestine (SW480, CYP24A1 8%) and skin (HaCaT, CYP24A1 7%) cells. The X-ray crystal structural analysis of 4b in complex with rat VDR-ligand binding domain (LBD) showed the highest Cα positional shift from the 1/VDR-LBD complex at helix 11. Helix 11 of the 4b and 1 VDR-LBD complexes also showed significant differences in surface properties. These results suggest that 4b should be examined further as another candidate for a mild preventive osteoporosis agent.

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