› 6ad9

X-ray diffraction
2.2Å resolution

Crystal Structure of PPARgamma Ligand Binding Domain in complex with dibenzooxepine derivative compound-9

Released:
DOI: 10.2210/pdb6ad9/pdb
Model geometry
Fit model/data
PDB entry 6ad9 coloured by chain, front view.
PDB entry 6ad9 coloured by chain, side view.
PDB entry 6ad9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Development of Dihydrodibenzooxepine Peroxisome Proliferator-Activated Receptor (PPAR) Gamma Ligands of a Novel Binding Mode as Anticancer Agents: Effective Mimicry of Chiral Structures by Olefinic E/ Z-Isomers.
Yamamoto K, Tamura T, Henmi K, Kuboyama T, Yanagisawa A, Matsubara M, Takahashi Y, Suzuki M, Saito JI, Ueno K, Shuto S
J Med Chem 61 10067-10083 (2018)
PMID: 30351933

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153377 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Peroxisome proliferator-activated receptor gamma Chain: A
Molecule details ›
Chain: A
Length: 287 amino acids
Theoretical weight: 32.69 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P37231 (Residues: 223-505; Coverage: 56%)
Gene names: NR1C3, PPARG
Sequence domains: Ligand-binding domain of nuclear hormone receptor
Structure domains: Retinoid X Receptor
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha Chain: B
Molecule details ›
Chain: B
Length: 12 amino acids
Theoretical weight: 1.27 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q9UBK2 (Residues: 141-152; Coverage: 2%)
Gene names: LEM6, PGC1, PGC1A, PPARGC1, PPARGC1A

Ligands and Environments

1 bound ligand:
Ligand KK4 1 x KK4
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P21
Unit cell:
a: 43.73Å b: 54.338Å c: 66.77Å
α: 90° β: 108.61° γ: 90°
R-values:
R R work R free
0.187 0.185 0.24
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Analogues of Anticancer Natural Products: Chiral Aspects.
Valentová et al. (2023)
1 more