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
-
- 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