Fluorine in PDB 7vwg: Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Alpha/Delta Dual Agonist JKPL38

The structure of Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta Ligand Binding Domain in Complex with A Synthetic Alpha/Delta Dual Agonist JKPL38, PDB code: 7vwg 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)	42.58 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.5, 94.314, 96.247, 90, 97.37, 90
R / Rfree (%)	20 / 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 Alpha/Delta Dual Agonist JKPL38 (pdb code 7vwg). 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 Alpha/Delta Dual Agonist JKPL38, PDB code: 7vwg:
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 Alpha/Delta Dual Agonist JKPL38


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 Alpha/Delta Dual Agonist JKPL38 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:44.7 occ:1.00 F30 A:820502 0.0 44.7 1.0 C20 A:820502 1.3 40.1 1.0 F32 A:820502 2.1 42.5 1.0 F31 A:820502 2.1 43.5 1.0 C17 A:820502 2.4 34.8 1.0 C18 A:820502 2.7 41.5 1.0 C16 A:820502 3.6 33.5 1.0 CG2 A:VAL348 3.8 45.2 1.0 CG1 A:VAL281 3.9 32.1 1.0 CG2 A:VAL281 3.9 29.4 1.0 CB A:VAL348 4.0 37.5 1.0 C19 A:820502 4.1 35.6 1.0 CG1 A:VAL348 4.2 50.6 1.0 CD2 A:LEU353 4.2 42.3 1.0 CB A:VAL281 4.4 30.0 1.0 CD1 A:LEU255 4.7 42.8 1.0 C15 A:820502 4.7 38.9 1.0 CA A:VAL281 4.9 38.0 1.0 CE2 A:PHE352 4.9 46.4 1.0 C14 A:820502 4.9 43.4 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 Alpha/Delta Dual Agonist JKPL38


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 Alpha/Delta Dual Agonist JKPL38 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:43.5 occ:1.00 F31 A:820502 0.0 43.5 1.0 C20 A:820502 1.3 40.1 1.0 F32 A:820502 2.1 42.5 1.0 F30 A:820502 2.1 44.7 1.0 C17 A:820502 2.4 34.8 1.0 C16 A:820502 3.1 33.5 1.0 C18 A:820502 3.3 41.5 1.0 CD A:ARG284 3.4 38.5 1.0 CB A:ARG284 3.5 30.3 1.0 CG A:ARG284 3.6 33.9 1.0 CG2 A:VAL281 4.0 29.4 1.0 CA A:VAL281 4.1 38.0 1.0 CG1 A:VAL281 4.2 32.1 1.0 CH2 A:TRP264 4.3 45.5 1.0 CB A:VAL281 4.3 30.0 1.0 C15 A:820502 4.3 38.9 1.0 CD1 A:LEU255 4.4 42.8 1.0 C19 A:820502 4.5 35.6 1.0 NE A:ARG284 4.5 45.8 1.0 O A:VAL281 4.6 35.2 1.0 CZ2 A:TRP264 4.7 33.5 1.0 C A:VAL281 4.9 33.5 1.0 CA A:ARG284 4.9 36.2 1.0 C14 A:820502 4.9 43.4 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 Alpha/Delta Dual Agonist JKPL38


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 Alpha/Delta Dual Agonist JKPL38 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:42.5 occ:1.00 F32 A:820502 0.0 42.5 1.0 C20 A:820502 1.3 40.1 1.0 F30 A:820502 2.1 44.7 1.0 F31 A:820502 2.1 43.5 1.0 C17 A:820502 2.4 34.8 1.0 C16 A:820502 2.8 33.5 1.0 CH2 A:TRP264 3.2 45.5 1.0 C18 A:820502 3.5 41.5 1.0 CZ2 A:TRP264 3.9 33.5 1.0 CG1 A:VAL341 4.0 31.2 1.0 C15 A:820502 4.2 38.9 1.0 CZ3 A:TRP264 4.3 44.4 1.0 CG2 A:VAL341 4.3 44.5 1.0 CD A:ARG284 4.3 38.5 1.0 CD1 A:ILE249 4.3 36.3 1.0 CB A:VAL341 4.4 41.6 1.0 CB A:VAL348 4.4 37.5 1.0 CD1 A:LEU255 4.4 42.8 1.0 CG1 A:VAL348 4.5 50.6 1.0 C19 A:820502 4.7 35.6 1.0 CG2 A:VAL348 4.8 45.2 1.0 C14 A:820502 4.9 43.4 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 Alpha/Delta Dual Agonist JKPL38


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 Alpha/Delta Dual Agonist JKPL38 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:38.7 occ:1.00 F30 B:820501 0.0 38.7 1.0 C20 B:820501 1.3 39.2 1.0 F32 B:820501 2.1 41.2 1.0 F31 B:820501 2.1 39.3 1.0 C17 B:820501 2.4 28.0 1.0 C18 B:820501 2.7 37.4 1.0 CG1 B:VAL281 3.5 25.8 1.0 CG2 B:VAL281 3.6 28.8 1.0 C16 B:820501 3.6 31.2 1.0 CG2 B:VAL348 3.9 39.2 1.0 CD2 B:LEU353 4.0 32.5 1.0 CB B:VAL281 4.1 32.1 1.0 C19 B:820501 4.1 31.3 1.0 CB B:VAL348 4.4 33.7 1.0 CG1 B:VAL348 4.5 37.0 1.0 CA B:VAL281 4.6 31.7 1.0 CE2 B:PHE352 4.7 30.0 1.0 C15 B:820501 4.7 33.4 1.0 CD1 B:LEU255 4.9 37.3 1.0 C14 B:820501 4.9 32.6 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 Alpha/Delta Dual Agonist JKPL38


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 Alpha/Delta Dual Agonist JKPL38 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:39.3 occ:1.00 F31 B:820501 0.0 39.3 1.0 C20 B:820501 1.3 39.2 1.0 F32 B:820501 2.1 41.2 1.0 F30 B:820501 2.1 38.7 1.0 C17 B:820501 2.4 28.0 1.0 C16 B:820501 3.0 31.2 1.0 CD B:ARG284 3.4 35.2 1.0 C18 B:820501 3.4 37.4 1.0 CB B:ARG284 3.6 25.3 1.0 CG B:ARG284 3.8 34.9 1.0 CH2 B:TRP264 4.0 45.2 1.0 CG2 B:VAL281 4.2 28.8 1.0 CA B:VAL281 4.3 31.7 1.0 C15 B:820501 4.3 33.4 1.0 CG1 B:VAL281 4.3 25.8 1.0 CD1 B:LEU255 4.5 37.3 1.0 CB B:VAL281 4.5 32.1 1.0 NE B:ARG284 4.5 44.1 1.0 CZ2 B:TRP264 4.5 39.6 1.0 C19 B:820501 4.6 31.3 1.0 O B:VAL281 4.7 27.6 1.0 CZ3 B:TRP264 4.9 49.2 1.0 C14 B:820501 4.9 32.6 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 Alpha/Delta Dual Agonist JKPL38


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 Alpha/Delta Dual Agonist JKPL38 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:41.2 occ:1.00 F32 B:820501 0.0 41.2 1.0 C20 B:820501 1.3 39.2 1.0 F31 B:820501 2.1 39.3 1.0 F30 B:820501 2.1 38.7 1.0 C17 B:820501 2.4 28.0 1.0 C16 B:820501 2.9 31.2 1.0 C18 B:820501 3.4 37.4 1.0 CH2 B:TRP264 3.6 45.2 1.0 CG1 B:VAL341 3.9 23.0 1.0 CB B:VAL348 4.0 33.7 1.0 CG1 B:VAL348 4.2 37.0 1.0 CZ2 B:TRP264 4.2 39.6 1.0 C15 B:820501 4.2 33.4 1.0 CD1 B:ILE249 4.3 32.3 1.0 CG2 B:VAL348 4.3 39.2 1.0 CG2 B:VAL341 4.3 33.5 1.0 CB B:VAL341 4.4 33.1 1.0 CZ3 B:TRP264 4.6 49.2 1.0 C19 B:820501 4.6 31.3 1.0 CD1 B:LEU255 4.7 37.3 1.0 CD B:ARG284 4.8 35.2 1.0 C14 B:820501 4.9 32.6 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