5Z5S: PPARgamma-LBD

Crystal structure of the PPARgamma-LBD complexed with compound 13ab. Determined by X-ray diffraction at 1.8 Å resolution. Released 17 Oct 2018.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,478
Mol. weight: 34.98 kDa
Ligands: RTE
Released: 17 Oct 2018

Explore 5Z5S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Z5S contains 15 α-helices and 4 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: 14 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	207-225	19
α-helix	230-237	8
α-helix	244-246	3
β-strand	247-249	3	1
α-helix	252-261	10
α-helix	277-300	24
α-helix	306-308	3
α-helix	311-332	22
β-strand	334-335	2	1
β-strand	338-341	4	1
β-strand	346-349	4	1
α-helix	350-354	5
α-helix	357	1
α-helix	365-375	11
α-helix	381-392	12
α-helix	403-424	22
α-helix	431-457	27
α-helix	467-473	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-14	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peroxisome proliferator-activated receptor gamma	A	protein	283	Homo sapiens	P37231 (AlphaFold model)
Peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha	C	protein	19	Homo sapiens	Q9UBK2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5Z5S_1 Peroxisome proliferator-activated receptor gamma (chains A)
MRGSHHHHHHGPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNS
LMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQ
VTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKF
NALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAK
LLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

Sequence of entity 2 (C), FASTA

>5Z5S_2 Peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (chains C)
QEAEEPSLLKKLLLAPANT

Ligands and cofactors

ID	Name	Formula	Copies
RTE	3-{[6-(4-chloro-3-fluorophenoxy)-1-methyl-1H-benzimidazol-2-yl]methoxy}benzoic…	C22 H16 Cl F N2 O4	1

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

Primary citation

Discovery of DS-6930, a potent selective PPAR gamma modulator. Part I: Lead identification. Shinozuka, T., Tsukada, T., Fujii, K. et al. Bioorg Med Chem (2018) 26:5079-5098. DOI 10.1016/j.bmc.2018.09.006 · PubMed

Other PDB entries of the same protein (UniProt P37231 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9F7W 1.25 Å, Human PPARgamma ligand binding domain in complex with co-activator 1alpha peptide and…
8BF1 1.36 Å, High-resolution structure of unliganded PPAR gamma in complex with the peptide PGC-1 alpha
9V8G 1.39 Å, PPARgamma ligand-binding domain in complex with PG08-NL
9V8H 1.39 Å, PPARgamma ligand-binding domain in complex with PG08-NL and rosiglitazone
8FKC 1.42 Å, Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and…
6MS7 1.43 Å, Peroxisome proliferator-activated receptor gamma ligand binding domain in complex with a…
9V8D 1.44 Å, PPARgamma ligand-binding domain in complex with PG08
3U9Q 1.52 Å, Ligand binding domain of PPARgamma complexed with Decanoic Acid and PGC-1a peptide
8B94 1.55 Å, Crystal structure of PPARG and NCOR2 with BAY-5516, an inverse agonist
8DKV 1.59 Å, PPARg bound to JTP-426467 and Co-R peptide
3B1M 1.6 Å, Crystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative…
3V9V 1.6 Å, Crystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative…

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