SMTL ID : 9qx6.1

Crystal structure of RXR alpha LBD bound to a synthetic agonist FN537 and a coactivator fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 01: (6R,6aR,7S,10R,10aS)-6-(3,5-bis(trifluoromethyl)phenyl)-5,6,6a,7,8,9,10,10a-octahydro-7,10-methanophenanthridine-3-carboxylic acid

01.1: 22 residues within 4Å: Chain A: I.41, A.44, A.45, Q.48, W.78, N.79, L.82, I.83, F.86, R.89, I.97, L.99, A.100, V.115, I.118, F.119, V.122, C.205, H.208, L.209, F.212 Ligands: 02.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.41, A:A.45, A:Q.48, A:W.78, A:L.82, A:I.83, A:F.86, A:F.86, A:L.99, A:L.209 Hydrogen bonds: A:A.100 Water bridges: A:F.86 Salt bridges: A:R.89 Halogen bonds: A:C.205

1 x 02: 6S,6aS,7R,10S,10aR)-6-(3,5-bis(trifluoromethyl)phenyl)-5,6,6a,7,8,9,10,10a-octahydro-7,10-methanophenanthridine-3-carboxylic acid

02.2: 22 residues within 4Å: Chain A: I.41, A.44, A.45, Q.48, W.78, N.79, L.82, I.83, F.86, R.89, I.97, L.99, A.100, V.115, I.118, F.119, V.122, C.205, H.208, L.209, F.212 Ligands: 01.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.41, A:A.45, A:W.78, A:N.79, A:L.82, A:I.83, A:F.86, A:F.86, A:F.86, A:L.99, A:I.118, A:L.209 Hydrogen bonds: A:A.100 Water bridges: A:F.86 Salt bridges: A:R.89 Halogen bonds: A:C.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nawa, F. et al., Development of an RXR Agonist Scaffold with Pronounced Homodimer Preference. J.Med.Chem. (2025)

Release Date

2025-08-13

Peptides

Retinoic acid receptor RXR-alpha: A
Nuclear receptor coactivator 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Retinoic acid receptor RXR-alpha

Nuclear receptor coactivator 2

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