SMTL ID : 9gya.1

Vitamin D Receptor in complex with Sila-e

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-2-2-mer

Ligands

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

ACT.1: 8 residues within 4Å: Chain A: T.23, Y.24, D.25, Y.28, Y.113, K.117, R.151 Ligands: 01.2 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 ACT.3: 8 residues within 4Å: Chain C: T.23, Y.24, D.25, Y.28, Y.113, K.117, R.151 Ligands: 01.4 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.24, C:Y.28 Hydrogen bonds: C:D.25, C:Y.113 Salt bridges: C:K.117, C:R.151

2 x 01: (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R})-5-dimethylsilylpent-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.145, 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 Ligands: ACT.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.107, A:L.110, A:I.145, A:I.148, A:W.163, A:W.163, A:V.177, A:L.186, A:L.190 Hydrogen bonds: A:S.114, A:R.151, A:S.155 01.4: 21 residues within 4Å: Chain C: Y.24, L.104, L.107, L.110, V.111, S.114, I.145, 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 Ligands: ACT.3 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.107, C:L.110, C:I.145, C:I.148, C:W.163, C:W.163, C:V.177, C:L.186, C:L.190 Hydrogen bonds: C:S.114, C:R.151, C: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: 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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