5KYJ: Oxysterols receptor LXR-beta

Brain penetrant liver X receptor (LXR) modulators based on a 2,4,5,6-tetrahydropyrrolo[3,4-c]pyrazole core. Determined by X-ray diffraction at 2.8 Å resolution. Released 21 Sept 2016.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,565
Mol. weight: 122.28 kDa
Ligands: 6Y8
Released: 21 Sept 2016

Explore 5KYJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KYJ contains 49 α-helices and 10 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	222-244	23
α-helix	251-253	3
α-helix	257-258	2
α-helix	262-287	26
α-helix	297-318	22
β-strand	320-321	2	1
β-strand	326-329	4	1
β-strand	333-336	4	1
α-helix	337-342	6
α-helix	347-363	17
α-helix	367-378	12
α-helix	389-410	22
α-helix	417-444	28
α-helix	451-456	6
α-helix	470-476	7

Chain B: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	301-310	10
α-helix	335-355	21
α-helix	365-387	23
β-strand	394-396	3	2
β-strand	402-404	3	2
α-helix	405-410	6
α-helix	414-420	7
α-helix	421-426	6
α-helix	427-430	4
α-helix	435-446	12
α-helix	457-478	22
α-helix	485-490	6
α-helix	492-511	20
α-helix	520-526	7
α-helix	536-541	6

Chain E: 11 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	222-244	23
α-helix	251-253	3
α-helix	262-287	26
α-helix	297-318	22
β-strand	320-321	2	3
β-strand	326-329	4	3
β-strand	333-336	4	3
α-helix	337-342	6
α-helix	347-363	17
α-helix	367-378	12
α-helix	389-410	22
α-helix	417-444	28
α-helix	451-456	6
α-helix	469-476	8

Chain F: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	301-310	10
α-helix	335-355	21
α-helix	365-387	23
β-strand	394-396	3	4
β-strand	402-404	3	4
α-helix	405-410	6
α-helix	414-420	7
α-helix	421-426	6
α-helix	427-431	5
α-helix	435-446	12
α-helix	457-478	22
α-helix	485-490	6
α-helix	493-511	19
α-helix	520-525	6
α-helix	536-541	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Oxysterols receptor LXR-beta	A, E	protein	287	Homo sapiens	P55055 (AlphaFold model)
Retinoic acid receptor RXR-beta	B, F	protein	256	Homo sapiens	P28702 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>5KYJ_1 Oxysterols receptor LXR-beta (chains A, E)
MGSSHHHHHHSSGLVPRGSHMGEGVQLTAAQELMIQQLVAAQLQCNKRSFSDQPKVTPWP
LGADPASGSASQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIML
LETARRYNHETECITFLKDFTYSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALL
IAINIFSADRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSS
VHSEQVFALRLQDKKLPPLLSEIWDVHEGSGSGSHKILHRLLQDSSS

Sequence of entity 2 (B, F), FASTA

>5KYJ_2 Retinoic acid receptor RXR-beta (chains B, F)
HMGAPEEMPVDRILEAELAVEQKSDQGVEGPGGTGGSGSSPNDPVTNICQAADKQLFTLV
EWAKRIPHFSSLPLDDQVILLRAGWNELLIASFSHRSIDVRDGILLATGLHVHRNSAHSA
GVGAIFDRVLTELVSKMRDMRMDKTELGCLRAIILFNPDAKGLSNPSEVEVLREKVYASL
ETYCKQKYPEQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAGSG
SGSHKILHRLLQDSSS

Ligands and cofactors

ID	Name	Formula	Copies
6Y8	(6~{R})-5-(5-fluoranyl-2-methoxy-pyrimidin-4-yl)-2-(3-methylsulfonylphenyl)-6-p…	C20 H22 F N5 O3 S	2

Primary citation

Brain penetrant liver X receptor (LXR) modulators based on a 2,4,5,6-tetrahydropyrrolo[3,4-c]pyrazole core. Tice, C.M., Noto, P.B., Fan, K.Y. et al. Bioorg Med Chem Lett (2016) 26:5044-5050. DOI 10.1016/j.bmcl.2016.08.089 · PubMed

Other PDB entries of the same protein (UniProt P55055 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6S5K 1.6 Å, LXRbeta ligand binding domain in complex with small molecule inhibitors
6S4N 1.9 Å, LXRbeta ligand binding domain in comlpex with small molecule inhibitors
6S4T 2.0 Å, LXRbeta ligand binding domain in comlpex with small molecule inhibitors
4RAK 2.04 Å, Crystal structure of nuclear receptor subfamily 1, group h, member 2 (lxrb) complexed…
1PQ9 2.1 Å, Human lxr beta hormone receptor complexed with T0901317 complex
1UPV 2.1 Å, Crystal structure of the human Liver X receptor beta ligand binding domain in complex…
3L0E 2.3 Å, X-ray crystal structure of a Potent Liver X Receptor Modulator
1PQ6 2.4 Å, Human lxr beta hormone receptor / GW3965 complex
1UPW 2.4 Å, Crystal structure of the human Liver X receptor beta ligand binding domain in complex…
3KFC 2.4 Å, Complex Structure of LXR with an agonist
5JY3 2.4 Å, Crystal structure of lxrbeta (nuclear receptor subfamily 1, group H, member 2) complexed…
4DK7 2.45 Å, Crystal structure of LXR ligand binding domain in complex with full agonist 1

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