Fluorine in PDB 7vwh: Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Agonist JKPL39

The structure of Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Agonist JKPL39, PDB code: 7vwh 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 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.588, 94.139, 96.184, 90, 96.64, 90
R / Rfree (%)	20.5 / 24

The binding sites of Fluorine atom in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Agonist JKPL39 (pdb code 7vwh). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Agonist JKPL39, PDB code: 7vwh:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Agonist JKPL39


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 JKPL39 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:37.8 occ:1.00 F30 A:82K501 0.0 37.8 1.0 C20 A:82K501 1.3 37.0 1.0 F32 A:82K501 2.1 39.5 1.0 F31 A:82K501 2.1 39.4 1.0 C17 A:82K501 2.4 27.5 1.0 C18 A:82K501 2.7 27.8 1.0 CG1 A:VAL281 3.4 31.7 1.0 C16 A:82K501 3.6 32.6 1.0 CG2 A:VAL281 3.7 36.0 1.0 CG2 A:VAL348 3.9 35.4 1.0 C19 A:82K501 4.1 36.2 1.0 CB A:VAL281 4.1 37.1 1.0 CD2 A:LEU353 4.2 31.8 1.0 CB A:VAL348 4.3 35.1 1.0 CG1 A:VAL348 4.5 34.6 1.0 CD1 A:LEU255 4.5 36.2 1.0 CA A:VAL281 4.7 31.5 1.0 CE2 A:PHE352 4.7 35.7 1.0 C15 A:82K501 4.8 35.8 1.0 C14 A:82K501 4.9 38.4 1.0

Fluorine binding site 2 out of 6 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Agonist JKPL39


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 JKPL39 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:39.4 occ:1.00 F31 A:82K501 0.0 39.4 1.0 C20 A:82K501 1.3 37.0 1.0 F32 A:82K501 2.1 39.5 1.0 F30 A:82K501 2.1 37.8 1.0 C17 A:82K501 2.4 27.5 1.0 C16 A:82K501 3.0 32.6 1.0 CD A:ARG284 3.4 39.2 1.0 C18 A:82K501 3.4 27.8 1.0 CB A:ARG284 3.5 34.1 1.0 CG A:ARG284 3.6 27.8 1.0 CH2 A:TRP264 4.1 48.1 1.0 CG2 A:VAL281 4.1 36.0 1.0 CG1 A:VAL281 4.2 31.7 1.0 CA A:VAL281 4.2 31.5 1.0 C15 A:82K501 4.3 35.8 1.0 CD1 A:LEU255 4.3 36.2 1.0 CB A:VAL281 4.4 37.1 1.0 NE A:ARG284 4.5 38.8 1.0 CZ2 A:TRP264 4.6 49.5 1.0 C19 A:82K501 4.6 36.2 1.0 O A:VAL281 4.8 29.4 1.0 CZ3 A:TRP264 4.9 44.1 1.0 OE2 A:GLU259 4.9 40.5 1.0 C14 A:82K501 5.0 38.4 1.0 CA A:ARG284 5.0 26.4 1.0

Fluorine binding site 3 out of 6 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Agonist JKPL39


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 JKPL39 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:39.5 occ:1.00 F32 A:82K501 0.0 39.5 1.0 C20 A:82K501 1.3 37.0 1.0 F31 A:82K501 2.1 39.4 1.0 F30 A:82K501 2.1 37.8 1.0 C17 A:82K501 2.3 27.5 1.0 C16 A:82K501 2.9 32.6 1.0 CH2 A:TRP264 3.4 48.1 1.0 C18 A:82K501 3.4 27.8 1.0 CG1 A:VAL341 4.0 34.6 1.0 CD1 A:ILE249 4.1 34.1 1.0 CG2 A:VAL341 4.1 31.7 1.0 CZ2 A:TRP264 4.1 49.5 1.0 C15 A:82K501 4.2 35.8 1.0 CB A:VAL348 4.3 35.1 1.0 CB A:VAL341 4.3 38.0 1.0 CZ3 A:TRP264 4.3 44.1 1.0 CG1 A:VAL348 4.4 34.6 1.0 CD1 A:LEU255 4.5 36.2 1.0 CG2 A:VAL348 4.5 35.4 1.0 C19 A:82K501 4.6 36.2 1.0 CD A:ARG284 4.7 39.2 1.0 C14 A:82K501 4.9 38.4 1.0

Fluorine binding site 4 out of 6 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Agonist JKPL39


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 JKPL39 within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:33.8 occ:1.00 F30 B:82K503 0.0 33.8 1.0 C20 B:82K503 1.3 31.6 1.0 F31 B:82K503 2.1 37.9 1.0 F32 B:82K503 2.1 36.5 1.0 C17 B:82K503 2.4 30.8 1.0 C18 B:82K503 2.7 30.0 1.0 C16 B:82K503 3.6 36.4 1.0 CG2 B:VAL348 3.7 30.3 1.0 CG1 B:VAL281 3.8 24.5 1.0 CG2 B:VAL281 3.9 29.5 1.0 C19 B:82K503 4.1 36.1 1.0 CD2 B:LEU353 4.1 29.9 1.0 CB B:VAL348 4.2 30.6 1.0 CG1 B:VAL348 4.3 33.0 1.0 CB B:VAL281 4.4 28.6 1.0 CD1 B:LEU255 4.6 34.9 1.0 CE2 B:PHE352 4.6 33.5 1.0 C15 B:82K503 4.7 33.5 1.0 CA B:VAL281 4.9 26.1 1.0 C14 B:82K503 5.0 29.6 1.0

Fluorine binding site 5 out of 6 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Agonist JKPL39


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 JKPL39 within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:37.9 occ:1.00 F31 B:82K503 0.0 37.9 1.0 C20 B:82K503 1.3 31.6 1.0 F32 B:82K503 2.1 36.5 1.0 F30 B:82K503 2.1 33.8 1.0 C17 B:82K503 2.3 30.8 1.0 C16 B:82K503 3.1 36.4 1.0 C18 B:82K503 3.3 30.0 1.0 CB B:ARG284 3.5 35.3 1.0 CD B:ARG284 3.6 35.4 1.0 CG B:ARG284 3.7 29.3 1.0 CG2 B:VAL281 4.1 29.5 1.0 CA B:VAL281 4.1 26.1 1.0 CG1 B:VAL281 4.2 24.5 1.0 CH2 B:TRP264 4.3 40.6 1.0 C15 B:82K503 4.3 33.5 1.0 CB B:VAL281 4.4 28.6 1.0 CD1 B:LEU255 4.4 34.9 1.0 C19 B:82K503 4.5 36.1 1.0 O B:VAL281 4.5 31.9 1.0 NE B:ARG284 4.7 47.4 1.0 C B:VAL281 4.9 32.7 1.0 CZ2 B:TRP264 4.9 36.8 1.0 CA B:ARG284 4.9 23.2 1.0 C14 B:82K503 4.9 29.6 1.0 CD2 B:HIS280 5.0 30.5 1.0

Fluorine binding site 6 out of 6 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Agonist JKPL39


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 JKPL39 within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:36.5 occ:1.00 F32 B:82K503 0.0 36.5 1.0 C20 B:82K503 1.3 31.6 1.0 F31 B:82K503 2.1 37.9 1.0 F30 B:82K503 2.1 33.8 1.0 C17 B:82K503 2.3 30.8 1.0 C16 B:82K503 2.8 36.4 1.0 CH2 B:TRP264 3.2 40.6 1.0 C18 B:82K503 3.5 30.0 1.0 CG1 B:VAL341 4.1 21.2 1.0 CZ3 B:TRP264 4.1 48.4 1.0 CZ2 B:TRP264 4.1 36.8 1.0 C15 B:82K503 4.2 33.5 1.0 CG2 B:VAL341 4.2 31.8 1.0 CB B:VAL341 4.3 28.7 1.0 CB B:VAL348 4.4 30.6 1.0 CD1 B:ILE249 4.4 34.8 1.0 CG1 B:VAL348 4.5 33.0 1.0 CD1 B:LEU255 4.5 34.9 1.0 CD B:ARG284 4.5 35.4 1.0 CG2 B:VAL348 4.6 30.3 1.0 C19 B:82K503 4.6 36.1 1.0 C14 B:82K503 4.9 29.6 1.0 CB B:ARG284 5.0 35.3 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