SMTL ID : 5zwf.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 9KR: (E,7R)-7-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-2-en-4-one(Covalent)

9KR.1: 16 residues within 4Å: Chain A: Y.38, Y.42, L.77, V.78, S.81, I.115, R.118, S.119, S.122, W.130, C.132, V.144, H.149, L.153, H.241, L.248 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.38, A:L.77, A:V.78, A:I.115, A:W.130, A:V.144, A:V.144, A:L.153, A:L.248 Hydrogen bonds: A:R.118, A:S.122, A:S.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshizawa, M. et al., Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands. J. Med. Chem. (2018)

Release Date

2018-07-18

Peptides

Vitamin D3 receptor: A
13-meric peptide from DRIP205 NR2 BOX peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Vitamin D3 receptor

13-meric peptide from DRIP205 NR2 BOX peptide

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