Fluorine in PDB 7vwf: Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP204

The structure of Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP204, PDB code: 7vwf 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)	42.60 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.557, 94.248, 96.308, 90, 97.33, 90
R / Rfree (%)	20.2 / 21.8

The binding sites of Fluorine atom in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP204 (pdb code 7vwf). 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 Agonist TIPP204, PDB code: 7vwf:
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 Agonist TIPP204


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 Agonist TIPP204 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:31.5 occ:1.00 F29 A:K55502 0.0 31.5 1.0 C15 A:K55502 1.4 28.3 1.0 C16 A:K55502 2.3 30.2 1.0 C14 A:K55502 2.4 26.7 1.0 N27 A:K55502 2.6 27.6 1.0 C13 A:K55502 2.9 30.0 1.0 SG A:CYS285 3.3 29.8 1.0 CD2 A:LEU339 3.4 39.6 1.0 O33 A:K55502 3.5 32.3 1.0 C17 A:K55502 3.6 25.4 1.0 C19 A:K55502 3.6 28.5 1.0 C12 A:K55502 4.0 24.6 1.0 CD1 A:LEU353 4.1 32.7 1.0 C18 A:K55502 4.1 26.1 1.0 O28 A:K55502 4.1 34.5 1.0 C21 A:K55502 4.2 35.3 1.0 C22 A:K55502 4.2 41.3 1.0 C9 A:K55502 4.3 27.5 1.0 CD2 A:LEU353 4.5 35.9 1.0 C8 A:K55502 4.5 29.6 1.0 CG1 A:VAL281 4.7 30.3 1.0 C20 A:K55502 4.8 30.7 1.0 CB A:CYS285 4.8 23.3 1.0 F31 A:K55502 4.9 32.8 1.0 CG1 A:VAL348 4.9 34.3 1.0 CG A:LEU353 4.9 32.9 1.0 CG A:LEU339 4.9 40.3 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 Agonist TIPP204


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 Agonist TIPP204 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:34.4 occ:1.00 F30 A:K55502 0.0 34.4 1.0 C20 A:K55502 1.3 30.7 1.0 F31 A:K55502 2.1 32.8 1.0 F32 A:K55502 2.1 37.3 1.0 C17 A:K55502 2.3 25.4 1.0 C18 A:K55502 2.9 26.1 1.0 CH2 A:TRP264 3.2 41.1 1.0 C16 A:K55502 3.5 30.2 1.0 CZ2 A:TRP264 3.9 41.8 1.0 CD1 A:ILE249 4.0 40.2 1.0 CG1 A:VAL341 4.1 29.4 1.0 CZ3 A:TRP264 4.2 44.4 1.0 CB A:VAL348 4.2 33.2 1.0 C19 A:K55502 4.2 28.5 1.0 CG2 A:VAL341 4.3 42.6 1.0 CG2 A:VAL348 4.4 38.2 1.0 CB A:VAL341 4.4 37.7 1.0 CD1 A:LEU255 4.4 37.4 1.0 CG1 A:VAL348 4.5 34.3 1.0 CD A:ARG284 4.5 32.0 1.0 C15 A:K55502 4.6 28.3 1.0 C14 A:K55502 5.0 26.7 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 Agonist TIPP204


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 Agonist TIPP204 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:32.8 occ:1.00 F31 A:K55502 0.0 32.8 1.0 C20 A:K55502 1.3 30.7 1.0 F30 A:K55502 2.1 34.4 1.0 F32 A:K55502 2.1 37.3 1.0 C17 A:K55502 2.4 25.4 1.0 C16 A:K55502 2.7 30.2 1.0 CG2 A:VAL348 3.5 38.2 1.0 C18 A:K55502 3.6 26.1 1.0 CG1 A:VAL281 3.8 30.3 1.0 CG2 A:VAL281 4.0 30.4 1.0 CB A:VAL348 4.0 33.2 1.0 CD2 A:LEU353 4.1 35.9 1.0 C15 A:K55502 4.1 28.3 1.0 CG1 A:VAL348 4.2 34.3 1.0 CB A:VAL281 4.4 26.6 1.0 CD1 A:LEU255 4.7 37.4 1.0 CE2 A:PHE352 4.7 41.4 1.0 C19 A:K55502 4.8 28.5 1.0 F29 A:K55502 4.9 31.5 1.0 CA A:VAL281 4.9 28.6 1.0 C14 A:K55502 5.0 26.7 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 Agonist TIPP204


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 Agonist TIPP204 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:37.3 occ:1.00 F32 A:K55502 0.0 37.3 1.0 C20 A:K55502 1.3 30.7 1.0 F30 A:K55502 2.1 34.4 1.0 F31 A:K55502 2.1 32.8 1.0 C17 A:K55502 2.3 25.4 1.0 C18 A:K55502 3.0 26.1 1.0 C16 A:K55502 3.4 30.2 1.0 CD A:ARG284 3.5 32.0 1.0 CB A:ARG284 3.7 24.2 1.0 CG A:ARG284 3.8 27.8 1.0 CH2 A:TRP264 4.1 41.1 1.0 CG2 A:VAL281 4.1 30.4 1.0 CG1 A:VAL281 4.2 30.3 1.0 CA A:VAL281 4.2 28.6 1.0 CD1 A:LEU255 4.3 37.4 1.0 C19 A:K55502 4.3 28.5 1.0 CB A:VAL281 4.4 26.6 1.0 C15 A:K55502 4.5 28.3 1.0 NE A:ARG284 4.6 38.2 1.0 CZ2 A:TRP264 4.6 41.8 1.0 O A:VAL281 4.7 26.5 1.0 CZ3 A:TRP264 4.9 44.4 1.0 C14 A:K55502 5.0 26.7 1.0 C A:VAL281 5.0 25.7 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 Agonist TIPP204


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 Agonist TIPP204 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:26.3 occ:1.00 F29 B:K55502 0.0 26.3 1.0 C15 B:K55502 1.4 23.5 1.0 C16 B:K55502 2.3 25.6 1.0 C14 B:K55502 2.4 21.1 1.0 N27 B:K55502 2.7 25.4 1.0 C13 B:K55502 2.9 24.4 1.0 SG B:CYS285 3.3 25.7 1.0 CD2 B:LEU339 3.5 31.9 1.0 O33 B:K55502 3.5 26.5 1.0 C17 B:K55502 3.6 20.3 1.0 C19 B:K55502 3.6 23.5 1.0 C12 B:K55502 4.0 22.5 1.0 O28 B:K55502 4.1 33.7 1.0 C18 B:K55502 4.1 24.3 1.0 C22 B:K55502 4.1 33.9 1.0 CD1 B:LEU353 4.2 26.0 1.0 C21 B:K55502 4.2 34.2 1.0 C9 B:K55502 4.3 21.8 1.0 C8 B:K55502 4.5 24.7 1.0 CD1 B:ILE364 4.5 34.9 1.0 CD2 B:LEU353 4.5 26.1 1.0 CG1 B:VAL281 4.7 24.2 1.0 C20 B:K55502 4.8 27.9 1.0 CB B:CYS285 4.8 23.3 1.0 F31 B:K55502 4.9 29.1 1.0 C23 B:K55502 5.0 26.9 1.0 CG B:LEU339 5.0 27.9 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 Agonist TIPP204


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 Agonist TIPP204 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:33.3 occ:1.00 F30 B:K55502 0.0 33.3 1.0 C20 B:K55502 1.3 27.9 1.0 F32 B:K55502 2.1 30.6 1.0 F31 B:K55502 2.1 29.1 1.0 C17 B:K55502 2.3 20.3 1.0 C18 B:K55502 2.9 24.3 1.0 CH2 B:TRP264 3.1 42.4 1.0 C16 B:K55502 3.5 25.6 1.0 CZ2 B:TRP264 3.7 38.6 1.0 CG1 B:VAL341 3.9 28.4 1.0 CG2 B:VAL341 4.2 29.9 1.0 CZ3 B:TRP264 4.2 45.6 1.0 CB B:VAL348 4.2 28.0 1.0 C19 B:K55502 4.2 23.5 1.0 CD1 B:ILE249 4.2 39.2 1.0 CB B:VAL341 4.3 30.8 1.0 CG2 B:VAL348 4.4 32.2 1.0 CG1 B:VAL348 4.4 26.6 1.0 CD B:ARG284 4.6 36.6 1.0 C15 B:K55502 4.6 23.5 1.0 CD1 B:LEU255 4.7 38.8 1.0 C14 B:K55502 5.0 21.1 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 Agonist TIPP204


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 Agonist TIPP204 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:29.1 occ:1.00 F31 B:K55502 0.0 29.1 1.0 C20 B:K55502 1.3 27.9 1.0 F30 B:K55502 2.1 33.3 1.0 F32 B:K55502 2.1 30.6 1.0 C17 B:K55502 2.4 20.3 1.0 C16 B:K55502 2.7 25.6 1.0 CG2 B:VAL348 3.6 32.2 1.0 C18 B:K55502 3.6 24.3 1.0 CG1 B:VAL281 3.7 24.2 1.0 CD2 B:LEU353 4.0 26.1 1.0 CG2 B:VAL281 4.0 25.9 1.0 C15 B:K55502 4.1 23.5 1.0 CB B:VAL348 4.1 28.0 1.0 CG1 B:VAL348 4.3 26.6 1.0 CB B:VAL281 4.4 24.3 1.0 CE2 B:PHE352 4.7 30.9 1.0 C19 B:K55502 4.8 23.5 1.0 CD1 B:LEU255 4.9 38.8 1.0 F29 B:K55502 4.9 26.3 1.0 CA B:VAL281 4.9 25.8 1.0 C14 B:K55502 5.0 21.1 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 Agonist TIPP204


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 Agonist TIPP204 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:30.6 occ:1.00 F32 B:K55502 0.0 30.6 1.0 C20 B:K55502 1.3 27.9 1.0 F30 B:K55502 2.1 33.3 1.0 F31 B:K55502 2.1 29.1 1.0 C17 B:K55502 2.3 20.3 1.0 C18 B:K55502 3.0 24.3 1.0 C16 B:K55502 3.4 25.6 1.0 CD B:ARG284 3.5 36.6 1.0 CB B:ARG284 3.7 25.5 1.0 CG B:ARG284 3.8 25.3 1.0 CH2 B:TRP264 4.0 42.4 1.0 CG1 B:VAL281 4.1 24.2 1.0 CG2 B:VAL281 4.2 25.9 1.0 CA B:VAL281 4.2 25.8 1.0 C19 B:K55502 4.3 23.5 1.0 CB B:VAL281 4.4 24.3 1.0 CD1 B:LEU255 4.4 38.8 1.0 CZ2 B:TRP264 4.4 38.6 1.0 C15 B:K55502 4.5 23.5 1.0 NE B:ARG284 4.6 36.1 1.0 O B:VAL281 4.7 24.7 1.0 CZ3 B:TRP264 4.9 45.6 1.0 C14 B:K55502 5.0 21.1 1.0 C B:VAL281 5.0 24.3 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