SMTL ID : 9gyk.1

Vitamin D receptor in complex with Sila-f

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-mer

Ligands

2 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 ACT.3: 7 residues within 4Å: Chain C: T.23, Y.24, D.25, Y.28, Y.113, K.117, R.151 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~{S},3~{a}~{S},7~{a}~{S})-7~{a}-methyl-1-(4-trimethylsilylbuta-1,3-diynyl)-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol

01.2: 19 residues within 4Å: Chain A: Y.24, L.104, L.107, A.108, V.111, S.114, I.148, R.151, S.152, S.155, W.163, C.165, V.177, A.180, H.182, L.190, H.272, Y.276, L.279 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.24, A:L.107, A:V.111, A:I.148, A:W.163, A:V.177, A:L.190 Hydrogen bonds: A:Y.24, A:S.114, A:R.151, A:S.155 01.4: 19 residues within 4Å: Chain C: Y.24, L.104, L.107, A.108, V.111, S.114, I.148, R.151, S.152, S.155, W.163, C.165, V.177, A.180, H.182, L.190, H.272, Y.276, L.279 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.24, C:L.107, C:V.111, C:I.148, C:W.163, C:V.177, 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

Related Entries With Identical Sequence