5ZWF

Target information

RCSB PDB
5ZWF
Title
Covalent bond formation between histidine of Vitamin D receptor (VDR) and a full agonist having a enone with a beta methyl group via conjugate addition reaction
Method
X-RAY DIFFRACTION
Resolution
2.1
Classification
HORMONE
Organism
Rattus norvegicus, Homo sapiens
Protein
Vitamin D3 receptor (P13053)    Looking for covalent inhibitors of this target ?
Year
2018
Publication Title
Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands
Abstract

We designed and synthesized vitamin D analogues with an electrophile as covalent modifiers for the vitamin D receptor (VDR). Novel vitamin D analogues 1-4 have an electrophilic enone group at the side chain for conjugate addition to His301 or His393 in the VDR. All compounds showed specific VDR-binding potency and agonistic activity. Covalent bond formations of 1-4 with the ligand-binding domain (LBD) of VDR were evaluated by electrospray ionization mass spectrometry. All compounds were shown to covalently bind to the VDR-LBD, and the abundance of VDR-LBD corresponding conjugate adducts of 1-4 increased with incubation time. Enone compounds 1 and 2 showed higher reactivity than the ene-ynone 3 and dienone 4 compounds. Furthermore, we successfully obtained cocrystals of VDR-LBD with analogues 1-4. X-ray crystallographic analysis showed a covalent bond with His301 in VDR-LBD. We successfully synthesized vitamin D analogues that form a covalent bond with VDR-LBD.

External Link
RCSB PDB





Ligand information

HET
9KR
Chain ID
A
HET Number
501
Molecular Formula
C27H40O3
Structure
2D structure
IUPAC Name
(E,7R)-7-[(1R,3aS,4E,7aR)-4-[2-[(3R,5R)-3,5-dihydroxy-4-methylene-cyclohexylidene]ethylidene]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-2-en-4-one
InChI
InChI=1S/C27H40O3/c1-5-7-22(28)12-9-18(2)23-13-14-24-21(8-6-15-27(23,24)4)11-10-20-16-25(29)19(3)26(30)17-20/h5,7,10-11,18,23-26,29-30H,3,6,8-9,12-17H2,1-2,4H3/b7-5+,21-11+/t18-,23-,24+,25-,26-,27-/m1/s1
InChI Key
VGMKRRGYTONKLW-FOWSJJJVSA-N
Canonical SMILES
C/C=C/C(=O)CC[C@@H](C)[C@H]1CC[C@H]([C@@]12C)/C(CCC2)=C/C=C3\C[C@@H](O)C(=C)[C@H](O)C3
Bioactivity data
No bioactivity data available for this ligand.

Covalent Binding

Warhead
Michael Acceptor
Reaction Mechanism
Michael Addition
Residue
HIS : 301
Residue Chain
A
Interactions
Pharmacophore Model