5K13: RAR alpha ligand-binding domain

Crystal structure of the RAR alpha ligand-binding domain in complex with an antagonist. Determined by X-ray diffraction at 1.85 Å resolution. Released 22 Jun 2016.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,032
Mol. weight: 28.16 kDa
Ligands: 6Q7
Released: 22 Jun 2016

Explore 5K13 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5K13 contains 15 α-helices and 5 β-strands across 1 chain. 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: 15 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	182-196	15
α-helix	202-204	3
β-strand	208	1	1
α-helix	222-245	24
α-helix	249-251	3
α-helix	254-274	21
β-strand	277-278	2	2
β-strand	283-285	3	2
β-strand	290	1	1
β-strand	291-293	3	2
α-helix	294-297	4
α-helix	298-302	5
α-helix	303-305	3
α-helix	306-316	11
α-helix	317-319	3
α-helix	323-334	12
α-helix	345-366	22
α-helix	373-401	29
α-helix	403-405	3
α-helix	410-414	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoic acid receptor alpha	A	protein	246	Homo sapiens	P10276 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5K13_1 Retinoic acid receptor alpha (chains A)
TPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTV
EFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNA
GFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDRVDMLQEPLLEALK
VYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLENSEGL
DTLSGQ

Ligands and cofactors

ID	Name	Formula	Copies
6Q7	4-{5-(3-tert-butylphenyl)-1-[4-(methylsulfonyl)phenyl]-1H-pyrazol-3-yl}benzoic…	C27 H26 N2 O4 S	1

Primary citation

Identification of potent and selective retinoic acid receptor gamma (RAR gamma ) antagonists for the treatment of osteoarthritis pain using structure based drug design. Hughes, N.E., Bleisch, T.J., Jones, S.A. et al. Bioorg Med Chem Lett (2016) 26:3274-3277. DOI 10.1016/j.bmcl.2016.05.056 · PubMed

Other PDB entries of the same protein (UniProt P10276 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GFE 1.58 Å, hRAR LBD protein in complex with AM580 agonist ligand and a stapled peptide
1DSZ 1.7 Å, Structure of the rxr/rar DNA-binding domain heterodimer in complex with the retinoic…
3KMR 1.8 Å, Crystal structure of RARalpha ligand binding domain in complex with an agonist ligand…
7WQQ 1.9 Å, Retinoic acid receptor alpha mutant - N299H
3KMZ 2.1 Å, Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist…
9GFI 2.1 Å, hRAR alpha LBD-AM580 complex with staple peptide
6XWG 2.4 Å, Crystal Structure of the Human RXR/RAR DNA-Binding Domain Heterodimer Bound to the Human…
7APO 2.4 Å, Crystal structure of RARalpha ligand binding domain in complex with a fragment of the…
1DKF 2.5 Å, Crystal structure of a heterodimeric complex of rar and rxr ligand-binding domains
7AOS 2.55 Å, crystal structure of the RARalpha/RXRalpha ligand binding domain heterodimer in complex…
3A9E 2.75 Å, Crystal structure of a mixed agonist-bound RAR-alpha and antagonist-bound RXR-alpha…
4DQM 2.75 Å, Revealing a marine natural product as a novel agonist for retinoic acid receptors with a…

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