Fluorine in PDB 5y7x: Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta in Complexed with A Potent and Selective Agonist

The structure of Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta in Complexed with A Potent and Selective Agonist, PDB code: 5y7x was solved by H.L.Kim, J.W.Chin, S.J.Cho, J.Y.Song, H.S.Yoon, J.H.Bae, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.66 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.766, 93.896, 96.871, 90.00, 97.40, 90.00
R / Rfree (%)	20.5 / 23.1

The structure of Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta in Complexed with A Potent and Selective Agonist also contains other interesting chemical elements:

Potassium	(K)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Fluorine atom in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta in Complexed with A Potent and Selective Agonist (pdb code 5y7x). 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 in Complexed with A Potent and Selective Agonist, PDB code: 5y7x:
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 in Complexed with A Potent and Selective Agonist


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 in Complexed with A Potent and Selective Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:49.6 occ:1.00 F01 A:8RR501 0.0 49.6 1.0 C02 A:8RR501 1.4 43.5 1.0 F03 A:8RR501 2.2 50.9 1.0 F04 A:8RR501 2.2 48.2 1.0 C05 A:8RR501 2.4 40.2 1.0 C30 A:8RR501 2.6 39.0 1.0 CG2 A:VAL312 3.6 30.2 1.0 C06 A:8RR501 3.7 39.0 1.0 CB A:VAL312 3.9 27.5 1.0 C29 A:8RR501 4.0 40.3 1.0 CG2 A:VAL245 4.2 30.3 1.0 CG1 A:VAL312 4.3 28.2 1.0 CG1 A:VAL245 4.3 27.0 1.0 CD2 A:LEU317 4.6 27.7 1.0 CE2 A:PHE316 4.6 30.7 1.0 CD1 A:LEU219 4.7 38.6 1.0 C07 A:8RR501 4.8 39.3 1.0 CG2 A:ILE213 4.8 29.9 1.0 CB A:VAL245 4.8 27.3 1.0 C08 A:8RR501 4.9 41.0 1.0

Fluorine binding site 2 out of 6 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta in Complexed with A Potent and Selective Agonist


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 in Complexed with A Potent and Selective Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:50.9 occ:1.00 F03 A:8RR501 0.0 50.9 1.0 C02 A:8RR501 1.4 43.5 1.0 F01 A:8RR501 2.2 49.6 1.0 F04 A:8RR501 2.2 48.2 1.0 C05 A:8RR501 2.4 40.2 1.0 C06 A:8RR501 3.1 39.0 1.0 C30 A:8RR501 3.3 39.0 1.0 CB A:ARG248 3.5 26.9 1.0 CD A:ARG248 3.5 40.8 1.0 CG A:ARG248 3.7 30.1 1.0 CH2 A:TRP228 4.2 41.2 1.0 CG2 A:VAL245 4.3 30.3 1.0 CA A:VAL245 4.3 25.9 1.0 C07 A:8RR501 4.4 39.3 1.0 CD1 A:LEU219 4.4 38.6 1.0 CG1 A:VAL245 4.4 27.0 1.0 C29 A:8RR501 4.5 40.3 1.0 CB A:VAL245 4.6 27.3 1.0 CZ2 A:TRP228 4.7 41.8 1.0 NE A:ARG248 4.7 43.1 1.0 O A:VAL245 4.8 26.5 1.0 CA A:ARG248 4.9 27.2 1.0 C08 A:8RR501 4.9 41.0 1.0

Fluorine binding site 3 out of 6 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta in Complexed with A Potent and Selective Agonist


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 in Complexed with A Potent and Selective Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:48.2 occ:1.00 F04 A:8RR501 0.0 48.2 1.0 C02 A:8RR501 1.4 43.5 1.0 F01 A:8RR501 2.2 49.6 1.0 F03 A:8RR501 2.2 50.9 1.0 C05 A:8RR501 2.3 40.2 1.0 C06 A:8RR501 2.9 39.0 1.0 CH2 A:TRP228 3.1 41.2 1.0 C30 A:8RR501 3.4 39.0 1.0 CZ2 A:TRP228 3.7 41.8 1.0 CG1 A:VAL305 3.7 30.2 1.0 CG2 A:VAL305 3.9 32.2 1.0 CB A:VAL305 4.1 31.4 1.0 C07 A:8RR501 4.2 39.3 1.0 CZ3 A:TRP228 4.2 46.1 1.0 CD1 A:ILE213 4.3 35.0 1.0 CB A:VAL312 4.4 27.5 1.0 CD A:ARG248 4.5 40.8 1.0 C29 A:8RR501 4.6 40.3 1.0 CG1 A:VAL312 4.6 28.2 1.0 CG2 A:VAL312 4.8 30.2 1.0 C08 A:8RR501 4.9 41.0 1.0 CD1 A:LEU219 4.9 38.6 1.0

Fluorine binding site 4 out of 6 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta in Complexed with A Potent and Selective Agonist


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 in Complexed with A Potent and Selective Agonist within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:53.9 occ:1.00 F01 B:8RR501 0.0 53.9 1.0 C02 B:8RR501 1.4 50.6 1.0 F03 B:8RR501 2.2 53.7 1.0 F04 B:8RR501 2.2 55.5 1.0 C05 B:8RR501 2.4 46.1 1.0 C30 B:8RR501 2.7 43.5 1.0 CG2 B:VAL312 3.3 40.6 1.0 CG1 B:VAL312 3.5 38.2 1.0 C06 B:8RR501 3.6 43.2 1.0 CB B:VAL312 3.9 36.2 1.0 C29 B:8RR501 4.1 46.2 1.0 CG2 B:VAL245 4.5 36.1 1.0 CG1 B:VAL245 4.5 33.7 1.0 CD1 B:LEU219 4.6 40.1 1.0 CG2 B:ILE213 4.7 32.8 1.0 C07 B:8RR501 4.7 46.6 1.0 CD1 B:ILE213 4.8 39.7 1.0 CH2 B:TRP228 4.8 50.0 1.0 CE2 B:PHE316 4.8 43.2 1.0 CD2 B:LEU317 4.9 36.5 1.0 C08 B:8RR501 4.9 46.4 1.0 CG1 B:VAL305 5.0 38.1 1.0

Fluorine binding site 5 out of 6 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta in Complexed with A Potent and Selective Agonist


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 in Complexed with A Potent and Selective Agonist within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:53.7 occ:1.00 F03 B:8RR501 0.0 53.7 1.0 C02 B:8RR501 1.4 50.6 1.0 F01 B:8RR501 2.2 53.9 1.0 F04 B:8RR501 2.2 55.5 1.0 C05 B:8RR501 2.4 46.1 1.0 C06 B:8RR501 3.2 43.2 1.0 CB B:ARG248 3.2 31.5 1.0 C30 B:8RR501 3.2 43.5 1.0 CG B:ARG248 3.3 35.8 1.0 CD B:ARG248 4.1 41.6 1.0 CA B:VAL245 4.2 32.3 1.0 CG2 B:VAL245 4.3 36.1 1.0 CG1 B:VAL245 4.3 33.7 1.0 CH2 B:TRP228 4.3 50.0 1.0 C29 B:8RR501 4.4 46.2 1.0 C07 B:8RR501 4.4 46.6 1.0 CB B:VAL245 4.5 32.5 1.0 CD1 B:LEU219 4.5 40.1 1.0 O B:VAL245 4.6 31.8 1.0 CA B:ARG248 4.7 28.2 1.0 NE B:ARG248 4.7 48.3 1.0 CZ2 B:TRP228 4.8 50.0 1.0 C08 B:8RR501 4.9 46.4 1.0 C B:VAL245 4.9 31.1 1.0

Fluorine binding site 6 out of 6 in the Human Peroxisome Proliferator-Activated Receptor (Ppar) Delta in Complexed with A Potent and Selective Agonist


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 in Complexed with A Potent and Selective Agonist within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:55.5 occ:1.00 F04 B:8RR501 0.0 55.5 1.0 C02 B:8RR501 1.4 50.6 1.0 F01 B:8RR501 2.2 53.9 1.0 F03 B:8RR501 2.2 53.7 1.0 C05 B:8RR501 2.3 46.1 1.0 C06 B:8RR501 2.8 43.2 1.0 CH2 B:TRP228 2.9 50.0 1.0 CZ2 B:TRP228 3.4 50.0 1.0 C30 B:8RR501 3.5 43.5 1.0 CG2 B:VAL312 3.7 40.6 1.0 CG1 B:VAL305 3.9 38.1 1.0 CZ3 B:TRP228 4.0 53.3 1.0 CG2 B:VAL305 4.0 39.5 1.0 C07 B:8RR501 4.1 46.6 1.0 CB B:VAL305 4.1 40.1 1.0 CD1 B:ILE213 4.4 39.7 1.0 CB B:ARG248 4.6 31.5 1.0 CG B:ARG248 4.6 35.8 1.0 CD B:ARG248 4.6 41.6 1.0 C29 B:8RR501 4.7 46.2 1.0 CE2 B:TRP228 4.8 55.5 1.0 CD1 B:LEU219 4.8 40.1 1.0 CB B:VAL312 4.9 36.2 1.0 C08 B:8RR501 4.9 46.4 1.0

J.W.Chin, S.J.Cho. Design, Synthesis, and the X-Ray Co-Crystal Structure of Highly Potent, Selective, and Orally Bioavailable, Novel Peroxisome Proliferator-Activated Receptor Delta Agonists To Be Published.