Fluorine in PDB 2znq: Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP401

The structure of Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP401, PDB code: 2znq was solved by T.Oyama, Y.Hirakawa, N.Nagasawa, H.Miyachi, K.Morikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.35 / 2.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.172, 91.947, 96.361, 90.00, 98.01, 90.00
R / Rfree (%)	21.4 / 27.6

The binding sites of Fluorine atom in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP401 (pdb code 2znq). 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 Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP401, PDB code: 2znq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP401


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 TIPP401 within 5.0Å range: probe atom residue distance (Å) B Occ A:F922 b:31.7 occ:1.00 F26 A:401922 0.0 31.7 1.0 C15 A:401922 1.4 30.2 1.0 C16 A:401922 2.4 29.8 1.0 C14 A:401922 2.4 30.1 1.0 N24 A:401922 2.7 30.9 1.0 C13 A:401922 2.9 31.7 1.0 O30 A:401922 3.4 29.2 1.0 SG A:CYS285 3.5 26.8 1.0 C17 A:401922 3.7 31.1 1.0 C19 A:401922 3.7 28.7 1.0 CD2 A:LEU339 3.9 33.6 1.0 C12 A:401922 3.9 29.2 1.0 C21 A:401922 3.9 29.4 1.0 O25 A:401922 4.0 33.4 1.0 CD1 A:LEU339 4.0 30.6 1.0 C9 A:401922 4.2 27.9 1.0 C18 A:401922 4.2 29.1 1.0 CD2 A:LEU353 4.2 26.4 1.0 C8 A:401922 4.4 29.1 1.0 CG A:LEU339 4.5 31.8 1.0 CG A:LEU353 4.6 26.2 1.0 CD1 A:LEU353 4.7 23.2 1.0 C20 A:401922 5.0 31.9 1.0 CB A:CYS285 5.0 28.6 1.0 CG1 A:VAL281 5.0 22.3 1.0

Fluorine binding site 2 out of 8 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP401


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 TIPP401 within 5.0Å range: probe atom residue distance (Å) B Occ A:F922 b:33.5 occ:1.00 F27 A:401922 0.0 33.5 1.0 C20 A:401922 1.3 31.9 1.0 F29 A:401922 2.1 32.9 1.0 F28 A:401922 2.1 32.4 1.0 C17 A:401922 2.4 31.1 1.0 C18 A:401922 2.8 29.1 1.0 CG2 A:VAL348 3.5 30.9 1.0 CH2 A:TRP264 3.5 36.0 1.0 C16 A:401922 3.6 29.8 1.0 CG1 A:VAL341 4.0 30.3 1.0 CD A:ARG284 4.2 28.1 1.0 C19 A:401922 4.2 28.7 1.0 CD1 A:LEU255 4.2 27.2 1.0 CZ3 A:TRP264 4.3 39.0 1.0 CZ2 A:TRP264 4.4 37.2 1.0 CD1 A:ILE249 4.4 25.6 1.0 CG2 A:VAL341 4.4 26.7 1.0 CB A:VAL341 4.4 28.0 1.0 CB A:VAL348 4.7 29.6 1.0 C15 A:401922 4.8 30.2 1.0 CB A:ARG284 4.9 30.3 1.0 C14 A:401922 5.0 30.1 1.0 CG1 A:VAL348 5.0 29.4 1.0

Fluorine binding site 3 out of 8 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP401


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 TIPP401 within 5.0Å range: probe atom residue distance (Å) B Occ A:F922 b:32.4 occ:1.00 F28 A:401922 0.0 32.4 1.0 C20 A:401922 1.3 31.9 1.0 F27 A:401922 2.1 33.5 1.0 F29 A:401922 2.1 32.9 1.0 C17 A:401922 2.4 31.1 1.0 C16 A:401922 2.8 29.8 1.0 CG2 A:VAL348 3.1 30.9 1.0 CG1 A:VAL348 3.5 29.4 1.0 C18 A:401922 3.7 29.1 1.0 CB A:VAL348 3.9 29.6 1.0 CG1 A:VAL281 4.1 22.3 1.0 C15 A:401922 4.2 30.2 1.0 CE2 A:PHE352 4.4 30.3 1.0 CG2 A:VAL281 4.4 23.9 1.0 CD1 A:LEU353 4.5 23.2 1.0 CB A:VAL281 4.8 23.8 1.0 C19 A:401922 4.8 28.7 1.0 CD1 A:LEU255 4.8 27.2 1.0 CD2 A:LEU255 4.9 26.4 1.0 CG1 A:VAL341 4.9 30.3 1.0 CD2 A:PHE352 4.9 31.0 1.0 CG2 A:ILE249 5.0 22.6 1.0

Fluorine binding site 4 out of 8 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP401


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 TIPP401 within 5.0Å range: probe atom residue distance (Å) B Occ A:F922 b:32.9 occ:1.00 F29 A:401922 0.0 32.9 1.0 C20 A:401922 1.3 31.9 1.0 F27 A:401922 2.1 33.5 1.0 F28 A:401922 2.1 32.4 1.0 C17 A:401922 2.4 31.1 1.0 C18 A:401922 3.1 29.1 1.0 C16 A:401922 3.4 29.8 1.0 CG1 A:VAL281 3.8 22.3 1.0 CD A:ARG284 3.8 28.1 1.0 CG2 A:VAL281 3.9 23.9 1.0 CB A:ARG284 3.9 30.3 1.0 CA A:VAL281 3.9 24.5 1.0 CB A:VAL281 4.0 23.8 1.0 CG A:ARG284 4.3 28.9 1.0 C19 A:401922 4.4 28.7 1.0 CD2 A:LEU255 4.4 26.4 1.0 CD1 A:LEU255 4.5 27.2 1.0 O A:VAL281 4.5 25.7 1.0 C15 A:401922 4.6 30.2 1.0 C A:VAL281 4.7 25.7 1.0 N A:VAL281 4.9 25.0 1.0 CG2 A:VAL348 4.9 30.9 1.0 NE A:ARG284 5.0 30.1 1.0 CH2 A:TRP264 5.0 36.0 1.0

Fluorine binding site 5 out of 8 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP401


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 TIPP401 within 5.0Å range: probe atom residue distance (Å) B Occ B:F923 b:26.3 occ:1.00 F26 B:401923 0.0 26.3 1.0 C15 B:401923 1.4 26.7 1.0 C16 B:401923 2.4 24.5 1.0 C14 B:401923 2.4 27.7 1.0 N24 B:401923 2.7 30.4 1.0 C13 B:401923 2.9 29.6 1.0 O30 B:401923 3.4 29.2 1.0 SG B:CYS285 3.5 26.2 1.0 C19 B:401923 3.7 26.3 1.0 C17 B:401923 3.7 24.8 1.0 CD1 B:LEU339 3.8 28.3 1.0 C21 B:401923 3.9 32.6 1.0 C12 B:401923 3.9 29.0 1.0 O25 B:401923 4.0 31.6 1.0 CD2 B:LEU339 4.0 30.0 1.0 C18 B:401923 4.2 25.4 1.0 C9 B:401923 4.2 28.4 1.0 CD2 B:LEU353 4.4 23.2 1.0 C8 B:401923 4.4 28.9 1.0 CG B:LEU339 4.5 26.8 1.0 CD1 B:ILE364 4.6 25.6 1.0 CG B:LEU353 4.7 24.2 1.0 CG1 B:VAL281 4.9 23.4 1.0 CD1 B:LEU353 4.9 23.1 1.0 CB B:CYS285 4.9 25.4 1.0 C20 B:401923 5.0 25.1 1.0

Fluorine binding site 6 out of 8 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP401


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 TIPP401 within 5.0Å range: probe atom residue distance (Å) B Occ B:F923 b:27.9 occ:1.00 F27 B:401923 0.0 27.9 1.0 C20 B:401923 1.3 25.1 1.0 F28 B:401923 2.1 25.8 1.0 F29 B:401923 2.1 25.6 1.0 C17 B:401923 2.4 24.8 1.0 C18 B:401923 3.0 25.4 1.0 C16 B:401923 3.5 24.5 1.0 CD B:ARG284 3.5 28.1 1.0 CB B:ARG284 3.6 25.5 1.0 CG B:ARG284 4.0 24.9 1.0 CH2 B:TRP264 4.0 42.6 1.0 CA B:VAL281 4.2 25.6 1.0 CG1 B:VAL281 4.2 23.4 1.0 C19 B:401923 4.3 26.3 1.0 CD1 B:LEU255 4.4 27.6 1.0 CZ2 B:TRP264 4.5 41.9 1.0 CG2 B:VAL281 4.5 24.9 1.0 CB B:VAL281 4.6 25.9 1.0 O B:VAL281 4.6 25.8 1.0 NE B:ARG284 4.7 29.2 1.0 C15 B:401923 4.7 26.7 1.0 CZ3 B:TRP264 4.9 43.2 1.0 CG2 B:VAL348 4.9 27.1 1.0 C B:VAL281 4.9 25.6 1.0

Fluorine binding site 7 out of 8 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP401


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP401 within 5.0Å range: probe atom residue distance (Å) B Occ B:F923 b:25.8 occ:1.00 F28 B:401923 0.0 25.8 1.0 C20 B:401923 1.3 25.1 1.0 F27 B:401923 2.1 27.9 1.0 F29 B:401923 2.1 25.6 1.0 C17 B:401923 2.4 24.8 1.0 C18 B:401923 2.9 25.4 1.0 CH2 B:TRP264 3.0 42.6 1.0 CG2 B:VAL348 3.1 27.1 1.0 C16 B:401923 3.5 24.5 1.0 CZ2 B:TRP264 3.7 41.9 1.0 CG1 B:VAL341 3.8 28.6 1.0 CZ3 B:TRP264 4.1 43.2 1.0 CD1 B:ILE249 4.1 28.6 1.0 CB B:VAL341 4.3 27.8 1.0 CG2 B:VAL341 4.3 25.9 1.0 C19 B:401923 4.3 26.3 1.0 CB B:VAL348 4.5 26.9 1.0 CD1 B:LEU255 4.5 27.6 1.0 CD B:ARG284 4.6 28.1 1.0 C15 B:401923 4.7 26.7 1.0 CG1 B:VAL348 4.8 27.7 1.0

Fluorine binding site 8 out of 8 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP401


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP401 within 5.0Å range: probe atom residue distance (Å) B Occ B:F923 b:25.6 occ:1.00 F29 B:401923 0.0 25.6 1.0 C20 B:401923 1.3 25.1 1.0 F28 B:401923 2.1 25.8 1.0 F27 B:401923 2.1 27.9 1.0 C17 B:401923 2.4 24.8 1.0 C16 B:401923 2.8 24.5 1.0 CG2 B:VAL348 3.4 27.1 1.0 C18 B:401923 3.7 25.4 1.0 CG1 B:VAL348 3.8 27.7 1.0 CG1 B:VAL281 3.8 23.4 1.0 CB B:VAL348 4.2 26.9 1.0 CG2 B:VAL281 4.2 24.9 1.0 C15 B:401923 4.2 26.7 1.0 CB B:VAL281 4.5 25.9 1.0 CD1 B:LEU353 4.5 23.1 1.0 CD1 B:LEU255 4.7 27.6 1.0 CE2 B:PHE352 4.7 22.5 1.0 C19 B:401923 4.8 26.3 1.0 CA B:VAL281 4.8 25.6 1.0 CH2 B:TRP264 5.0 42.6 1.0

T.Oyama, K.Toyota, T.Waku, Y.Hirakawa, N.Nagasawa, J.Kasuga, Y.Hashimoto, H.Miyachi, K.Morikawa. Adaptability and Selectivity of Human Peroxisome Proliferator-Activated Receptor (Ppar) Pan Agonists Revealed From Crystal Structures Acta Crystallogr.,Sect.D V. 65 786 2009.
ISSN: ISSN 0907-4449
PubMed: 19622862
DOI: 10.1107/S0907444909015935