3OMK: Human FXR

Crystal structure of human FXR in complex with (2S)-2-[2-(4-chlorophenyl)-5,6-difluoro-1H-benzimidazol-1-yl]-2-cyclohexyl-N-(2-methylphenyl)ethanamide. Determined by X-ray diffraction at 1.9 Å resolution. Released 19 Jan 2011.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,256
Mol. weight: 58.77 kDa
Ligands: OMK
Released: 19 Jan 2011

Explore 3OMK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3OMK contains 26 α-helices and 0 β-strands across 4 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: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	251-264	14
α-helix	268-269	2
α-helix	270-279	10
α-helix	284-308	25
α-helix	312-314	3
α-helix	317-340	24
α-helix	348-357	10
α-helix	363-377	15
α-helix	383-394	12
α-helix	405-426	22
α-helix	433-456	24
α-helix	467-473	7

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	747-754	8

Chain C: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	251-264	14
α-helix	268-269	2
α-helix	270-279	10
α-helix	284-307	24
α-helix	312-314	3
α-helix	317-340	24
α-helix	348-357	10
α-helix	363-376	14
α-helix	383-394	12
α-helix	405-426	22
α-helix	433-456	24
α-helix	467-473	7

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	747-753	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bile acid receptor	A, C	protein	233	Homo sapiens	Q96RI1 (AlphaFold model)
peptide of Nuclear receptor coactivator 1	B, D	protein	14		Q15788 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3OMK_1 Bile acid receptor (chains A, C)
GSHMELTPDQQTLLHFIMDSYNKQRMPQEITNKILKEAFSAEENFLILTEMATNHVQVLV
EFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEARIRNSGISD
EYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLC
KIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDVQ

Sequence of entity 2 (B, D), FASTA

>3OMK_2 peptide of Nuclear receptor coactivator 1 (chains B, D)
KDHQLLRYLLDKDE

Ligands and cofactors

ID	Name	Formula	Copies
OMK	(2S)-2-[2-(4-chlorophenyl)-5,6-difluoro-1H-benzimidazol-1-yl]-2-cyclohexyl-N-(2…	C28 H26 Cl F2 N3 O	2

Primary citation

Optimization of a novel class of benzimidazole-based farnesoid X receptor (FXR) agonists to improve physicochemical and ADME properties. Richter, H.G.F., Benson, G.M., Bleicher, K.H. et al. Bioorg Med Chem Lett (2011) 21:1134-1140. DOI 10.1016/j.bmcl.2010.12.123 · 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
4OIV 1.7 Å, Structural basis for small molecule NDB as a selective antagonist of FXR
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

Browse structure collections

About this viewer

MolViewer shows 3OMK directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.