SMTL ID : 3dr1.1

Side-chain fluorine atoms of non-steroidal vitamin D3 analogs stabilize helix 12 of vitamin D receptor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: Q.233, D.234, C.237 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.237 MG.3: 3 residues within 4Å: Chain C: Q.233, D.234, C.237 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.237

2 x C5D: (1R,3R)-5-[(2E)-3-{(1S,3R)-2,2,3-trimethyl-3-[6,6,6-trifluoro-5-hydroxy-5-(trifluoromethyl)hex-3-yn-1-yl]cyclopentyl}prop-2-en-1-ylidene]cyclohexane-1,3-diol(Non-covalent)

C5D.2: 22 residues within 4Å: Chain A: Y.24, Y.28, L.104, A.108, L.110, V.111, S.114, R.151, S.152, S.155, W.163, C.165, V.177, A.180, H.182, L.190, H.272, Y.276, L.279, L.289, V.293, F.297 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.24, A:L.110, A:L.110, A:W.163, A:W.163, A:V.177, A:L.190 Hydrogen bonds: A:Y.24, A:R.151, A:R.151, A:S.155, A:H.272 Halogen bonds: A:A.180 C5D.4: 22 residues within 4Å: Chain C: Y.24, Y.28, L.104, A.108, L.110, V.111, S.114, R.151, S.152, S.155, W.163, C.165, V.177, A.180, H.182, L.190, H.272, Y.276, L.279, L.289, V.293, F.297 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.24, C:L.110, C:L.110, C:W.163, C:W.163, C:V.177, C:L.190 Hydrogen bonds: C:Y.24, C:Y.24, C:R.151, C:R.151, C:S.155, C:H.272 Halogen bonds: C:A.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eelen, G. et al., Superagonistic fluorinated vitamin D3 analogs stabilize helix 12 of the vitamin D receptor. Chem.Biol. (2008)

Release Date

2009-06-16

Peptides

Vitamin D3 receptor A: AC
SRC-1 (LXXLL motif) from Nuclear receptor coactivator 1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Vitamin D3 receptor A

SRC-1 (LXXLL motif) from Nuclear receptor coactivator 1

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