SMTL ID : 5zwh.1

Covalent bond formation between histidine of Vitamin D receptor (VDR) and a full agonist having an ene-ynone group via conjugate addition reaction

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 9KX: (2S)-2-[(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-4,6-diene-3-one(Covalent)

9KX.1: 19 residues within 4Å: Chain A: Y.38, Y.42, F.45, L.74, V.78, S.81, I.112, I.115, R.118, S.119, S.122, W.130, C.132, V.144, H.149, H.241, Y.245, L.248 Ligands: 9N9.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.45, A:V.78, A:I.112, A:I.115, A:W.130, A:V.144, A:Y.245, A:L.248 Hydrogen bonds: A:Y.38, A:R.118, A:R.118, A:S.122

1 x 9N9: (E,2S)-2-[(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-6-en-4-yn-3-one(Non-covalent)

9N9.2: 20 residues within 4Å: Chain A: Y.38, Y.42, F.45, L.71, A.75, V.78, S.81, I.112, I.115, M.116, R.118, S.119, S.122, W.130, C.132, V.144, H.149, L.153, L.157 Ligands: 9KX.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.38, A:L.71, A:I.112, A:W.130, A:V.144, A:L.157 Hydrogen bonds: A:Y.38, A:R.118, A:R.118, 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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