4OIV: Bile acid receptor

Structural basis for small molecule NDB as a selective antagonist of FXR. Determined by X-ray diffraction at 1.7 Å resolution. Released 25 Mar 2015.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,765
Mol. weight: 53.97 kDa
Ligands: XX9
Released: 25 Mar 2015

Explore 4OIV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4OIV contains 23 α-helices and 2 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 11 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	251-264	14
α-helix	284-308	25
α-helix	312-314	3
α-helix	317-342	26
α-helix	351-357	7
α-helix	363-377	15
α-helix	383-394	12
α-helix	405-426	22
α-helix	433-446	14
α-helix	450-455	6
β-strand	458-462	5	1
α-helix	468-470	3

Chain B: 12 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	251-264	14
α-helix	271-279	9
α-helix	284-308	25
α-helix	312-314	3
α-helix	317-340	24
α-helix	350-357	8
α-helix	363-378	16
α-helix	383-394	12
α-helix	405-426	22
α-helix	433-445	13
α-helix	450-455	6
β-strand	458-462	5	1
α-helix	468-470	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bile acid receptor	A, B	protein	226	Homo sapiens	Q96RI1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4OIV_1 Bile acid receptor (chains A, B)
ELTPDQQTLLHFIMDSYNKQRMPQEITNKILKEEFSAEENFLILTEMATNHVQVLVEFTK
KLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEERIRNSGISDEYIT
PMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQ
PENPQHFAELLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLEEIW

Ligands and cofactors

ID	Name	Formula	Copies
XX9	N-benzyl-N-(3-tert-butyl-4-hydroxyphenyl)-2,6-dichloro-4-(dimethylamino)benzami…	C26 H28 Cl2 N2 O2	2

Primary citation

Structural Basis for Small Molecule NDB (N-Benzyl-N-(3-(tert-butyl)-4-hydroxyphenyl)-2,6-dichloro-4-(dimethylamino) Benzamide) as a Selective Antagonist of Farnesoid X Receptor alpha (FXR alpha ) in Stabilizing the Homodimerization of the Receptor. Xu, X., Xu, X., Liu, P. et al. J Biol Chem (2015) 290:19888-19899. DOI 10.1074/jbc.M114.630475 · PubMed

Other PDB entries of the same protein (UniProt Q96RI1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6HL1 1.6 Å, Crystal Structure of Farnesoid X receptor (FXR) with bound NCoA-2 peptide and CDCA
6HL0 1.66 Å, Crystal Structure of Farnesoid X receptor (FXR) with bound NCoA-2 peptide
5Q0I 1.7 Å, Ligand binding to FARNESOID-X-RECEPTOR
1OSH 1.8 Å, A Chemical, Genetic, and Structural Analysis of the nuclear bile acid receptor FXR
5Q0K 1.8 Å, Ligand binding to FARNESOID-X-RECEPTOR
5Q0P 1.8 Å, Ligand binding to FARNESOID-X-RECEPTOR
5Q14 1.85 Å, Ligand binding to FARNESOID-X-RECEPTOR
5Q1E 1.85 Å, Ligand binding to FARNESOID-X-RECEPTOR
5Q0V 1.87 Å, Ligand binding to FARNESOID-X-RECEPTOR
5Q1D 1.89 Å, Ligand binding to FARNESOID-X-RECEPTOR
3BEJ 1.9 Å, Structure of human FXR in complex with MFA-1 and co-activator peptide
3L1B 1.9 Å, Complex Structure of FXR Ligand-binding domain with a tetrahydroazepinoindole compound

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