SMTL ID : 8pz9.1

Crystal structure of VDR in complex with D-Bishomo-1a,25-dihydroxyvitamin D3 Analog 55

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

hetero-2-2-mer

Ligands

2 x IFK: (1~{R},3~{R})-5-[(2~{E})-2-[(4~{a}~{R},5~{R},9~{a}~{S})-4~{a}-methyl-5-[(2~{R})-6-methyl-6-oxidanyl-heptan-2-yl]-3,4,5,8,9,9~{a}-hexahydro-2~{H}-benzo[7]annulen-1-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol(Non-covalent)

IFK.1: 20 residues within 4Å: Chain A: Y.24, Y.28, L.110, V.111, S.114, I.145, I.148, M.149, R.151, S.152, S.155, W.163, C.165, V.177, H.182, H.272, Y.276, L.279, L.289, F.297 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.24, A:L.110, A:I.145, A:I.148, A:W.163, A:V.177, A:Y.276, A:L.279, A:L.289, A:F.297 Hydrogen bonds: A:Y.24, A:Y.24, A:Y.28, A:R.151, A:R.151, A:S.155, A:H.272 IFK.2: 20 residues within 4Å: Chain C: Y.24, Y.28, L.110, V.111, S.114, I.145, I.148, M.149, R.151, S.152, S.155, W.163, C.165, V.177, H.182, H.272, Y.276, L.279, L.289, F.297 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:Y.24, C:L.110, C:I.145, C:I.148, C:W.163, C:V.177, C:Y.276, C:L.279, C:L.289, C:F.297 Hydrogen bonds: C:Y.24, C:R.151, C:R.151, C:S.155, C:H.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fabisiak, A. et al., Design, synthesis, and biological activity of D-bishomo-1 alpha ,25-dihydroxyvitamin D 3 analogs and their crystal structures with the vitamin D nuclear receptor. Eur.J.Med.Chem. (2024)

Release Date

2023-08-30

Peptides

Vitamin D3 receptor A: AC
Nuclear receptor coactivator 2: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Vitamin D3 receptor A

Nuclear receptor coactivator 2

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