Fluorine in PDB 8hf8: Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist V1

The structure of Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist V1, PDB code: 8hf8 was solved by L.Dai, H.B.Sun, H.L.Yuan, Z.Q.Feng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.26 / 2.11
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.795, 92.966, 96.715, 90, 96, 90
R / Rfree (%)	19.9 / 23

The binding sites of Fluorine atom in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist V1 (pdb code 8hf8). 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 Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist V1, PDB code: 8hf8:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist V1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist V1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:36.2 occ:1.00 F27 A:LOO501 0.0 36.2 1.0 C28 A:LOO501 1.3 35.7 1.0 F29 A:LOO501 2.1 36.7 1.0 F30 A:LOO501 2.3 40.6 1.0 C2 A:LOO501 2.3 32.2 1.0 C1 A:LOO501 2.8 33.3 1.0 CH2 A:TRP264 2.9 39.5 1.0 CZ3 A:TRP264 3.6 51.9 1.0 C3 A:LOO501 3.7 30.3 1.0 CD1 A:LEU255 3.7 45.9 1.0 CG2 A:VAL348 3.7 35.1 1.0 CD1 A:ILE249 3.7 40.4 1.0 CZ2 A:TRP264 3.8 48.1 1.0 C6 A:LOO501 4.3 29.4 1.0 CD A:ARG284 4.5 45.4 1.0 CG2 A:ILE249 4.6 38.7 1.0 CG2 A:VAL341 4.7 33.5 1.0 CG A:ARG284 4.7 46.6 1.0 CG1 A:VAL341 4.7 30.5 1.0 CB A:ARG284 4.8 30.0 1.0 CG1 A:VAL348 4.9 31.9 1.0 C4 A:LOO501 4.9 32.7 1.0 CB A:VAL341 4.9 38.0 1.0 CB A:VAL348 4.9 38.6 1.0 CE3 A:TRP264 4.9 55.5 1.0

Fluorine binding site 2 out of 6 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist V1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist V1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:36.7 occ:1.00 F29 A:LOO501 0.0 36.7 1.0 C28 A:LOO501 1.3 35.7 1.0 F27 A:LOO501 2.1 36.2 1.0 F30 A:LOO501 2.1 40.6 1.0 C2 A:LOO501 2.3 32.2 1.0 C1 A:LOO501 3.1 33.3 1.0 C3 A:LOO501 3.3 30.3 1.0 CB A:ARG284 3.7 30.0 1.0 CG A:ARG284 3.7 46.6 1.0 CG2 A:VAL281 3.7 23.5 1.0 CD1 A:LEU255 3.8 45.9 1.0 CA A:VAL281 4.0 34.6 1.0 CG1 A:VAL281 4.1 26.2 1.0 CB A:VAL281 4.1 27.8 1.0 CD A:ARG284 4.2 45.4 1.0 CD2 A:LEU255 4.4 40.6 1.0 C6 A:LOO501 4.4 29.4 1.0 CH2 A:TRP264 4.5 39.5 1.0 O A:VAL281 4.5 29.7 1.0 C4 A:LOO501 4.6 32.7 1.0 CG A:LEU255 4.7 42.4 1.0 C A:VAL281 4.8 27.4 1.0 N A:VAL281 5.0 27.6 1.0 C5 A:LOO501 5.0 30.7 1.0

Fluorine binding site 3 out of 6 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist V1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist V1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:40.6 occ:1.00 F30 A:LOO501 0.0 40.6 1.0 C28 A:LOO501 1.3 35.7 1.0 F29 A:LOO501 2.1 36.7 1.0 F27 A:LOO501 2.3 36.2 1.0 C2 A:LOO501 2.4 32.2 1.0 C3 A:LOO501 2.8 30.3 1.0 CG1 A:VAL348 3.5 31.9 1.0 CG2 A:VAL348 3.7 35.1 1.0 C1 A:LOO501 3.8 33.3 1.0 CE2 A:PHE352 3.8 33.3 1.0 CG2 A:VAL281 3.9 23.5 1.0 CG2 A:ILE249 4.0 38.7 1.0 CD1 A:LEU255 4.0 45.9 1.0 CB A:VAL348 4.2 38.6 1.0 C4 A:LOO501 4.3 32.7 1.0 CG1 A:VAL281 4.4 26.2 1.0 CD2 A:PHE352 4.5 33.1 1.0 CD1 A:ILE249 4.7 40.4 1.0 CB A:VAL281 4.7 27.8 1.0 CZ A:PHE352 4.7 33.9 1.0 CD2 A:LEU255 4.8 40.6 1.0 CB A:ILE249 4.8 44.9 1.0 CG A:LEU255 5.0 42.4 1.0 CD2 A:LEU353 5.0 26.7 1.0 C6 A:LOO501 5.0 29.4 1.0

Fluorine binding site 4 out of 6 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist V1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist V1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:40.4 occ:1.00 F27 B:LOO501 0.0 40.4 1.0 C28 B:LOO501 1.4 43.9 1.0 F30 B:LOO501 2.2 45.8 1.0 F29 B:LOO501 2.2 47.6 1.0 C2 B:LOO501 2.3 37.1 1.0 C1 B:LOO501 2.7 36.3 1.0 CG2 B:VAL281 3.6 40.2 1.0 CD1 B:LEU255 3.7 41.7 1.0 CG2 B:VAL348 3.7 51.5 1.0 C3 B:LOO501 3.7 41.1 1.0 CE2 B:PHE352 4.1 54.8 1.0 CG1 B:VAL281 4.2 46.4 1.0 C6 B:LOO501 4.2 40.8 1.0 CG1 B:VAL348 4.3 39.5 1.0 CG2 B:ILE249 4.4 38.7 1.0 CB B:VAL281 4.4 33.8 1.0 CD2 B:PHE352 4.6 48.7 1.0 CB B:VAL348 4.6 45.2 1.0 CD2 B:LEU353 4.8 42.1 1.0 CG B:LEU255 4.8 40.2 1.0 CA B:VAL281 4.9 37.7 1.0 CD2 B:LEU255 4.9 39.5 1.0 C4 B:LOO501 4.9 31.7 1.0

Fluorine binding site 5 out of 6 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist V1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist V1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:47.6 occ:1.00 F29 B:LOO501 0.0 47.6 1.0 C28 B:LOO501 1.4 43.9 1.0 F30 B:LOO501 2.2 45.8 1.0 F27 B:LOO501 2.2 40.4 1.0 C2 B:LOO501 2.3 37.1 1.0 C3 B:LOO501 3.0 41.1 1.0 CH2 B:TRP264 3.0 52.8 1.0 CG2 B:VAL348 3.3 51.5 1.0 C1 B:LOO501 3.5 36.3 1.0 CD1 B:ILE249 3.7 48.3 1.0 CZ3 B:TRP264 3.8 50.2 1.0 CD1 B:LEU255 3.8 41.7 1.0 CZ2 B:TRP264 4.0 51.5 1.0 CG2 B:VAL341 4.4 39.8 1.0 C4 B:LOO501 4.4 31.7 1.0 CG2 B:ILE249 4.5 38.7 1.0 CG1 B:VAL341 4.7 41.0 1.0 CB B:VAL348 4.7 45.2 1.0 CD B:ARG284 4.8 52.0 1.0 C6 B:LOO501 4.8 40.8 1.0 CB B:VAL341 4.9 42.2 1.0 CG1 B:ILE249 4.9 45.9 1.0 CB B:ILE249 4.9 42.1 1.0

Fluorine binding site 6 out of 6 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist V1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist V1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:45.8 occ:1.00 F30 B:LOO501 0.0 45.8 1.0 C28 B:LOO501 1.4 43.9 1.0 F29 B:LOO501 2.2 47.6 1.0 F27 B:LOO501 2.2 40.4 1.0 C2 B:LOO501 2.3 37.1 1.0 C3 B:LOO501 3.0 41.1 1.0 C1 B:LOO501 3.5 36.3 1.0 CD1 B:LEU255 3.7 41.7 1.0 CD B:ARG284 3.7 52.0 1.0 CB B:ARG284 3.7 43.8 1.0 CG B:ARG284 3.7 50.3 1.0 CH2 B:TRP264 3.9 52.8 1.0 CG2 B:VAL281 4.0 40.2 1.0 CA B:VAL281 4.2 37.7 1.0 OE2 B:GLU259 4.4 58.6 1.0 C4 B:LOO501 4.4 31.7 1.0 CZ3 B:TRP264 4.5 50.2 1.0 CB B:VAL281 4.5 33.8 1.0 CG1 B:VAL281 4.6 46.4 1.0 CD2 B:HIS280 4.7 39.1 1.0 NE B:ARG284 4.7 54.5 1.0 CZ2 B:TRP264 4.7 51.5 1.0 C6 B:LOO501 4.8 40.8 1.0 O B:VAL281 4.8 38.7 1.0 CG B:LEU255 5.0 40.2 1.0

Z.Feng, J.Xiang, G.Sun, H.Liu, Y.Wang, X.Liu, J.Feng, Q.Xu, X.Wen, H.Yuan, H.Sun, L.Dai. Discovery of the First Subnanomolar Ppar Alpha / Delta Dual Agonist For the Treatment of Cholestatic Liver Diseases. J.Med.Chem. V. 66 7331 2023.
ISSN: ISSN 0022-2623
PubMed: 37243609
DOI: 10.1021/ACS.JMEDCHEM.2C02123