SMTL ID : 9gyc.1

Vitamin D receptor in complex with Sila-d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 7 residues within 4Å: Chain A: T.23, Y.24, D.25, Y.28, Y.113, K.117, R.151 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.24, A:Y.28 Hydrogen bonds: A:D.25 Salt bridges: A:K.117, A:R.151

1 x 01: (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R})-5-[~{tert}-butyl(dimethyl)silyl]pent-4-yn-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol

01.2: 21 residues within 4Å: Chain A: Y.24, L.104, L.107, L.110, V.111, S.114, I.148, R.151, S.152, S.155, W.163, C.165, V.177, H.182, L.186, L.190, H.272, Y.276, L.279, L.289, F.297 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.24, A:L.104, A:L.107, A:L.110, A:L.110, A:I.148, A:W.163, A:W.163, A:W.163, A:V.177, A:L.186, A:L.190, A:L.289 Hydrogen bonds: A:Y.24, A:S.114, A:R.151, A:S.155, A:S.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loureiro, J. et al., First Sila-Vitamin D Analogues: Design, Synthesis, Structural Analysis and Biological Activity. J.Med.Chem. (2024)

Release Date

2024-12-11

Peptides

Vitamin D3 receptor A: A
Nuclear receptor coactivator 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Vitamin D3 receptor A

Nuclear receptor coactivator 2

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