SMTL ID : 5xpl.1

Crystal structure of VDR-LBD complexed with 22S-butyl-25-hydroxyphenyl-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 8C9: (4~{S})-4-[(1~{R})-1-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl )cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]ethyl]-1-(4-hydroxyphenyl)octan-1-one(Non-covalent)

8C9.1: 21 residues within 4Å: Chain A: Y.38, L.74, V.78, S.81, I.112, M.116, R.118, S.119, S.122, W.130, C.132, V.144, H.149, L.153, I.154, L.157, N.238, H.241, S.242, Y.245, F.266 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.38, A:L.74, A:V.78, A:I.112, A:I.112, A:W.130, A:V.144, A:L.153, A:I.154, A:L.157, A:H.241, A:Y.245, A:F.266, A:F.266 Hydrogen bonds: A:R.118, A:S.122, A:S.122 Water bridges: A:R.246 pi-Cation interactions: A:H.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kato, A. et al., Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action. J. Med. Chem. (2017)

Release Date

2018-06-06

Peptides

Vitamin D3 receptor: A
Nuclear receptor coactivator 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Vitamin D3 receptor

Nuclear receptor coactivator 2

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