3IPU: Benzisoxazole urea synthetic agonist

X-ray structure of benzisoxazole urea synthetic agonist bound to the LXR-alpha. Determined by X-ray diffraction at 2.4 Å resolution. Released 2 Jun 2010.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,297
Mol. weight: 72.5 kDa
Ligands: O40
Released: 2 Jun 2010

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

Secondary structure: helices and β-sheets

3IPU contains 26 α-helices and 6 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, 3 β-strands

Element	Residues	Length	Sheet
α-helix	208-227	20
α-helix	229-233	5
α-helix	236-238	3
α-helix	247-274	28
α-helix	283-304	22
β-strand	306-307	2	1
β-strand	312-314	3	1
β-strand	320-322	3	1
α-helix	323-328	6
α-helix	333-349	17
α-helix	353-364	12
α-helix	375-396	22
α-helix	403-430	28
α-helix	434-436	3
α-helix	437-443	7

Chain B: 11 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	208-227	20
α-helix	229-233	5
α-helix	247-273	27
α-helix	283-304	22
β-strand	306-307	2	2
β-strand	312-314	3	2
β-strand	320-321	2	2
α-helix	323-328	6
α-helix	333-349	17
α-helix	353-364	12
α-helix	375-396	22
α-helix	403-430	28
α-helix	434-436	3
α-helix	437-443	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	687-694	8

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	682-685	4
α-helix	687-694	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Oxysterols receptor LXR-alpha	A, B	protein	283	Homo sapiens	Q13133 (AlphaFold model)
Nuclear receptor coactivator 1	C, D	protein	25		Q15788 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3IPU_1 Oxysterols receptor LXR-alpha (chains A, B)
MKHQHQHQHQHQHQQPLQEEEQAHATSLPPRASSPPQILPQLSPEQLGMIEKLVAAQQQC
NRRSFSDRLRVTPWPMAPDPHSREARQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSRE
DQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDFAKAGLQVEFINPIFEFSR
AMNELQLNDAEFALLIAISIFSADRPNVQDQLQVERLQHTYVEALHAYVSIHHPHDRLMF
PRMLMKLVSLRTLSSVHSEQVFALRLQDKKLPPLLSEIWDVHE

Sequence of entity 2 (C, D), FASTA

>3IPU_2 Nuclear receptor coactivator 1 (chains C, D)
CPSSHSSLTERHKILHRLLQEGSPS

Ligands and cofactors

ID	Name	Formula	Copies
O40	4-{[methyl(3-{[7-propyl-3-(trifluoromethyl)-1,2-benzisoxazol-6-yl]oxy}propyl)ca…	C23 H24 F3 N3 O5	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

X-ray structures of the LXRalpha LBD in its homodimeric form and implications for heterodimer signaling. Fradera, X., Vu, D., Nimz, O. et al. J Mol Biol (2010) 399:120-132. DOI 10.1016/j.jmb.2010.04.005 · PubMed

Other PDB entries of the same protein (UniProt Q13133 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5HJS 1.72 Å, Identification of LXRbeta selective agonists for the treatment of Alzheimer's Disease
3IPQ 2.0 Å, X-ray structure of GW3965 synthetic agonist bound to the LXR-alpha
3IPS 2.26 Å, X-ray structure of benzisoxazole synthetic agonist bound to the LXR-alpha
5AVI 2.7 Å, Crystal structure of LXRalpha in complex with tert-butyl benzoate analog, compound 4
5AVL 2.8 Å, Crystal structure of LXRalpha in complex with tert-butyl benzoate analog, compound 32b
1UHL 2.9 Å, Crystal structure of the LXRalfa-RXRbeta LBD heterodimer

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