SMTL ID : 7cfo.1

Crystal structure of human RXRalpha ligand binding domain complexed with CBTF-EE.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

3 x WZ6: 1-[3-(2-ethoxyethoxy)-5,5,8,8-tetramethyl-6,7-dihydronaphthalen-2-yl]-2-(trifluoromethyl)benzimidazole-5-carboxylic acid(Non-covalent)

WZ6.1: 12 residues within 4Å: Chain A: I.49, A.53, W.86, L.90, L.214, L.217, F.219, F.220 Chain C: F.220, K.221, G.224 Ligands: WZ6.4 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:I.49, A:A.53, A:F.219, A:F.220, C:F.220 pi-Stacking: C:F.220 WZ6.2: 13 residues within 4Å: Chain B: C.50, A.53, Q.56, L.57, W.86, L.90, L.214, F.219, F.220, I.223 Chain D: L.217, F.220, F.231 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:L.217, D:F.220, D:F.231, B:Q.56, B:L.57, B:I.223 pi-Stacking: D:F.220, B:W.86, B:W.86 WZ6.4: 16 residues within 4Å: Chain A: L.217, F.220, I.228, F.231, L.232 Chain C: C.50, A.53, Q.56, L.57, R.83, W.86, L.214, F.219, F.220, I.223 Ligands: WZ6.1 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:L.217, A:F.220, A:I.228, A:F.231, A:F.231, A:L.232, C:R.83, C:L.214, C:F.220 pi-Stacking: A:F.220, C:W.86, C:W.86, C:F.220

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: E.133 Chain B: N.158, D.160, R.207 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.158, B:D.160, B:D.160, B:R.207, B:R.207 GOL.5: 5 residues within 4Å: Chain C: A.84, E.88, R.207, L.211 Chain D: S.208 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:A.84, C:E.88, C:R.207, D:S.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, M. et al., Discovery of a "Gatekeeper" Antagonist that Blocks Entry Pathway to Retinoid X Receptors (RXRs) without Allosteric Ligand Inhibition in Permissive RXR Heterodimers. J.Med.Chem. (2021)

Release Date

2021-01-06

Peptides

Retinoic acid receptor RXR-alpha: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Retinoic acid receptor RXR-alpha

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