SMTL ID : 5xpo.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 8BL: (5~{R})-5-[(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)cyclohexyl idene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]-1-(4-hydroxyphenyl)hexan-1-one(Non-covalent)

8BL.1: 16 residues within 4Å: Chain A: Y.38, L.71, L.74, V.78, S.81, R.118, S.119, S.122, W.130, C.132, V.144, A.147, H.149, Y.245, L.248, L.258 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.38, A:L.71, A:L.74, A:W.130, A:W.130, A:V.144, A:V.144, A:Y.245, A:L.248, A:L.258, A:L.258 Hydrogen bonds: A:R.118, A:S.122, A:S.122 pi-Stacking: A:H.149

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
Mediator of RNA polymerase II transcription subunit 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Vitamin D3 receptor

Mediator of RNA polymerase II transcription subunit 1

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