Fluorine in PDB 7vwe: Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122

The structure of Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122, PDB code: 7vwe was solved by T.Oyama, H.Miyachi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.57 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.123, 92.303, 96.088, 90, 98.06, 90
R / Rfree (%)	19.5 / 23.2

The binding sites of Fluorine atom in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122 (pdb code 7vwe). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122, PDB code: 7vwe:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:43.6 occ:1.00 F29 A:81O502 0.0 43.6 1.0 C15 A:81O502 1.4 46.4 1.0 C16 A:81O502 2.3 49.0 1.0 C4 A:81O502 2.4 50.6 1.0 N27 A:81O502 2.6 41.1 1.0 C13 A:81O502 2.9 46.8 1.0 SG A:CYS285 3.4 42.3 1.0 C17 A:81O502 3.6 47.5 1.0 C19 A:81O502 3.6 42.7 1.0 C12 A:81O502 3.9 38.2 1.0 C18 A:81O502 4.1 44.5 1.0 O28 A:81O502 4.1 41.4 1.0 CD2 A:LEU339 4.2 48.5 1.0 CD2 A:LEU353 4.3 41.1 1.0 C8 A:81O502 4.4 39.2 1.0 O33 A:81O502 4.4 45.6 1.0 CG1 A:VAL281 4.4 42.7 1.0 CD1 A:LEU353 4.4 47.8 1.0 CD1 A:LEU339 4.4 40.5 1.0 CG A:LEU353 4.5 44.0 1.0 C21 A:81O502 4.6 44.2 1.0 C9 A:81O502 4.6 39.8 1.0 CG A:LEU339 4.8 47.2 1.0 C20 A:81O502 4.8 46.5 1.0 F32 A:81O502 4.9 47.0 1.0 CG1 A:VAL348 4.9 42.1 1.0 CG1 A:VAL341 5.0 53.1 1.0

Fluorine binding site 2 out of 8 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:49.7 occ:1.00 F30 A:81O502 0.0 49.7 1.0 C20 A:81O502 1.3 46.5 1.0 F31 A:81O502 2.1 48.8 1.0 F32 A:81O502 2.1 47.0 1.0 C17 A:81O502 2.4 47.5 1.0 C18 A:81O502 2.9 44.5 1.0 C16 A:81O502 3.5 49.0 1.0 CD A:ARG284 3.5 55.1 1.0 CB A:ARG284 3.6 41.2 1.0 CD1 A:LEU255 3.7 45.5 1.0 CG A:ARG284 3.8 45.6 1.0 C19 A:81O502 4.2 42.7 1.0 OE2 A:GLU259 4.4 56.6 1.0 CA A:VAL281 4.6 45.9 1.0 CG2 A:VAL281 4.6 49.2 1.0 NE A:ARG284 4.6 65.2 1.0 C15 A:81O502 4.6 46.4 1.0 CG1 A:VAL281 4.7 42.7 1.0 CB A:VAL281 4.9 44.0 1.0 C4 A:81O502 5.0 50.6 1.0

Fluorine binding site 3 out of 8 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:48.8 occ:1.00 F31 A:81O502 0.0 48.8 1.0 C20 A:81O502 1.3 46.5 1.0 F32 A:81O502 2.1 47.0 1.0 F30 A:81O502 2.1 49.7 1.0 C17 A:81O502 2.4 47.5 1.0 C18 A:81O502 3.0 44.5 1.0 CG2 A:VAL348 3.3 49.0 1.0 C16 A:81O502 3.3 49.0 1.0 CD1 A:LEU255 3.8 45.5 1.0 CD1 A:ILE249 3.8 42.6 1.0 C19 A:81O502 4.3 42.7 1.0 CG2 A:VAL341 4.3 51.6 1.0 C15 A:81O502 4.5 46.4 1.0 CB A:VAL348 4.6 43.7 1.0 CG1 A:VAL341 4.7 53.1 1.0 CG1 A:VAL348 4.7 42.1 1.0 CG2 A:ILE249 4.7 39.7 1.0 CB A:VAL341 4.8 46.3 1.0 C4 A:81O502 5.0 50.6 1.0

Fluorine binding site 4 out of 8 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:47.0 occ:1.00 F32 A:81O502 0.0 47.0 1.0 C20 A:81O502 1.3 46.5 1.0 F31 A:81O502 2.1 48.8 1.0 F30 A:81O502 2.1 49.7 1.0 C17 A:81O502 2.3 47.5 1.0 C16 A:81O502 2.7 49.0 1.0 C18 A:81O502 3.6 44.5 1.0 CG2 A:VAL281 3.6 49.2 1.0 CG1 A:VAL281 3.7 42.7 1.0 CD1 A:LEU255 3.7 45.5 1.0 C15 A:81O502 4.1 46.4 1.0 CB A:VAL281 4.1 44.0 1.0 CG2 A:VAL348 4.2 49.0 1.0 CG1 A:VAL348 4.4 42.1 1.0 CA A:VAL281 4.5 45.9 1.0 CE2 A:PHE352 4.5 49.7 1.0 C19 A:81O502 4.7 42.7 1.0 F29 A:81O502 4.9 43.6 1.0 CB A:VAL348 4.9 43.7 1.0 C4 A:81O502 5.0 50.6 1.0 CG A:LEU255 5.0 51.6 1.0

Fluorine binding site 5 out of 8 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:38.3 occ:1.00 F29 B:81O502 0.0 38.3 1.0 C15 B:81O502 1.4 45.4 1.0 C16 B:81O502 2.3 44.5 1.0 C4 B:81O502 2.4 45.4 1.0 N27 B:81O502 2.6 40.7 1.0 C13 B:81O502 2.9 38.2 1.0 SG B:CYS285 3.5 42.1 1.0 C19 B:81O502 3.6 43.5 1.0 C17 B:81O502 3.6 45.5 1.0 CD2 B:LEU339 3.8 44.1 1.0 C12 B:81O502 3.9 41.1 1.0 C18 B:81O502 4.1 43.9 1.0 O28 B:81O502 4.1 41.4 1.0 CD2 B:LEU353 4.2 30.8 1.0 C8 B:81O502 4.3 35.2 1.0 O33 B:81O502 4.4 39.1 1.0 CD1 B:LEU353 4.5 38.3 1.0 CG B:LEU353 4.5 33.5 1.0 CG1 B:VAL281 4.5 33.6 1.0 C9 B:81O502 4.6 38.2 1.0 C21 B:81O502 4.6 37.5 1.0 CD1 B:LEU339 4.6 35.0 1.0 CD1 B:ILE364 4.8 35.7 1.0 CG B:LEU339 4.8 38.3 1.0 C20 B:81O502 4.8 43.6 1.0 F32 B:81O502 4.9 39.8 1.0 CB B:CYS285 5.0 39.8 1.0

Fluorine binding site 6 out of 8 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:43.0 occ:1.00 F30 B:81O502 0.0 43.0 1.0 C20 B:81O502 1.3 43.6 1.0 F31 B:81O502 2.1 45.3 1.0 F32 B:81O502 2.1 39.8 1.0 C17 B:81O502 2.4 45.5 1.0 C18 B:81O502 3.0 43.9 1.0 CG B:ARG284 3.3 48.4 1.0 C16 B:81O502 3.4 44.5 1.0 CB B:ARG284 3.5 47.0 1.0 CD1 B:LEU255 3.9 42.2 1.0 CH2 B:TRP264 3.9 58.3 1.0 C19 B:81O502 4.3 43.5 1.0 CD B:ARG284 4.3 51.2 1.0 CZ3 B:TRP264 4.4 59.3 1.0 C15 B:81O502 4.6 45.4 1.0 CG2 B:VAL281 4.6 40.2 1.0 CA B:VAL281 4.6 43.8 1.0 OE2 B:GLU259 4.6 60.0 1.0 CG1 B:VAL281 4.7 33.6 1.0 CZ2 B:TRP264 4.7 65.9 1.0 NE B:ARG284 4.9 61.4 1.0 CB B:VAL281 4.9 42.6 1.0 CD2 B:LEU255 5.0 39.4 1.0 C4 B:81O502 5.0 45.4 1.0 CA B:ARG284 5.0 40.6 1.0

Fluorine binding site 7 out of 8 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:45.3 occ:1.00 F31 B:81O502 0.0 45.3 1.0 C20 B:81O502 1.3 43.6 1.0 F30 B:81O502 2.1 43.0 1.0 F32 B:81O502 2.1 39.8 1.0 C17 B:81O502 2.4 45.5 1.0 C18 B:81O502 3.0 43.9 1.0 CG2 B:VAL348 3.1 41.8 1.0 C16 B:81O502 3.4 44.5 1.0 CH2 B:TRP264 3.5 58.3 1.0 CD1 B:ILE249 3.8 42.1 1.0 CD1 B:LEU255 3.9 42.2 1.0 CG2 B:VAL341 4.0 47.1 1.0 CG1 B:VAL341 4.2 39.1 1.0 CZ3 B:TRP264 4.2 59.3 1.0 C19 B:81O502 4.3 43.5 1.0 CB B:VAL341 4.4 43.0 1.0 CZ2 B:TRP264 4.4 65.9 1.0 CB B:VAL348 4.4 38.0 1.0 C15 B:81O502 4.6 45.4 1.0 CG2 B:ILE249 4.7 39.8 1.0 CG1 B:VAL348 4.8 37.8 1.0 CG1 B:ILE249 5.0 41.8 1.0 C4 B:81O502 5.0 45.4 1.0 CB B:ILE249 5.0 39.6 1.0

Fluorine binding site 8 out of 8 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Partial Agonist JK122 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:39.8 occ:1.00 F32 B:81O502 0.0 39.8 1.0 C20 B:81O502 1.3 43.6 1.0 F31 B:81O502 2.1 45.3 1.0 F30 B:81O502 2.1 43.0 1.0 C17 B:81O502 2.3 45.5 1.0 C16 B:81O502 2.7 44.5 1.0 C18 B:81O502 3.6 43.9 1.0 CG2 B:VAL348 3.7 41.8 1.0 CG1 B:VAL281 3.9 33.6 1.0 CG2 B:VAL281 3.9 40.2 1.0 CD1 B:LEU255 4.0 42.2 1.0 C15 B:81O502 4.1 45.4 1.0 CG1 B:VAL348 4.3 37.8 1.0 CB B:VAL281 4.4 42.6 1.0 CE2 B:PHE352 4.5 43.9 1.0 CB B:VAL348 4.6 38.0 1.0 C19 B:81O502 4.7 43.5 1.0 CD2 B:LEU255 4.7 39.4 1.0 CA B:VAL281 4.8 43.8 1.0 CD1 B:LEU353 4.8 38.3 1.0 F29 B:81O502 4.9 38.3 1.0 CG2 B:ILE249 4.9 39.8 1.0 C4 B:81O502 5.0 45.4 1.0

T.Oyama, K.Takiguchi, H.Miyachi. Crystal Structures of the Ligand-Binding Domain of Human Peroxisome Proliferator-Activated Receptor Delta in Complexes with Phenylpropanoic Acid Derivatives and A Pyridine Carboxylic Acid Derivative. Acta Crystallogr.,Sect.F V. 78 81 2022.
ISSN: ESSN 2053-230X
DOI: 10.1107/S2053230X22000449