Fluorine in PDB 2znp: Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP204

The structure of Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP204, PDB code: 2znp 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)	38.01 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.492, 93.149, 96.370, 90.00, 97.48, 90.00
R / Rfree (%)	23 / 28.8

The binding sites of Fluorine atom in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP204 (pdb code 2znp). 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 TIPP204, PDB code: 2znp:
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 TIPP204


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 TIPP204 within 5.0Å range: probe atom residue distance (Å) B Occ A:F922 b:32.2 occ:1.00 F29 A:K55922 0.0 32.2 1.0 C15 A:K55922 1.4 32.5 1.0 C14 A:K55922 2.4 31.9 1.0 C16 A:K55922 2.4 33.7 1.0 N27 A:K55922 2.6 35.6 1.0 C13 A:K55922 2.8 32.8 1.0 C19 A:K55922 3.7 32.1 1.0 C17 A:K55922 3.7 33.2 1.0 O33 A:K55922 3.8 40.4 1.0 SG A:CYS285 3.8 39.7 1.0 C12 A:K55922 3.8 37.0 1.0 O28 A:K55922 3.9 31.1 1.0 CD1 A:LEU339 3.9 40.9 1.0 C18 A:K55922 4.2 31.5 1.0 C22 A:K55922 4.2 40.5 1.0 CD2 A:LEU339 4.2 39.4 1.0 C21 A:K55922 4.4 41.6 1.0 C8 A:K55922 4.4 38.2 1.0 CD2 A:LEU353 4.4 39.6 1.0 C9 A:K55922 4.4 38.8 1.0 CG A:LEU339 4.7 40.1 1.0 CD1 A:LEU353 4.8 41.6 1.0 CG A:LEU353 4.8 40.7 1.0 CG1 A:VAL281 4.9 39.2 1.0 C20 A:K55922 5.0 33.4 1.0

Fluorine binding site 2 out of 8 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP204


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 TIPP204 within 5.0Å range: probe atom residue distance (Å) B Occ A:F922 b:34.4 occ:1.00 F30 A:K55922 0.0 34.4 1.0 C20 A:K55922 1.3 33.4 1.0 F32 A:K55922 2.1 34.2 1.0 F31 A:K55922 2.2 32.4 1.0 C17 A:K55922 2.4 33.2 1.0 C18 A:K55922 3.0 31.5 1.0 CG2 A:VAL348 3.1 45.0 1.0 C16 A:K55922 3.5 33.7 1.0 CG1 A:VAL341 3.9 39.8 1.0 CG2 A:VAL341 4.0 40.0 1.0 CB A:VAL341 4.1 39.7 1.0 CD1 A:LEU255 4.3 40.6 1.0 C19 A:K55922 4.3 32.1 1.0 CD A:ARG284 4.3 44.7 1.0 CD1 A:ILE249 4.3 40.0 1.0 CB A:VAL348 4.4 45.0 1.0 C15 A:K55922 4.7 32.5 1.0 CG1 A:VAL348 4.8 45.2 1.0 CG A:ARG284 4.8 42.6 1.0 NE A:ARG284 4.8 45.8 1.0 C14 A:K55922 5.0 31.9 1.0

Fluorine binding site 3 out of 8 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP204


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 TIPP204 within 5.0Å range: probe atom residue distance (Å) B Occ A:F922 b:32.4 occ:1.00 F31 A:K55922 0.0 32.4 1.0 C20 A:K55922 1.4 33.4 1.0 F30 A:K55922 2.2 34.4 1.0 F32 A:K55922 2.2 34.2 1.0 C17 A:K55922 2.4 33.2 1.0 C16 A:K55922 2.8 33.7 1.0 CG2 A:VAL348 3.3 45.0 1.0 C18 A:K55922 3.7 31.5 1.0 CG1 A:VAL348 3.8 45.2 1.0 CG1 A:VAL281 3.9 39.2 1.0 CB A:VAL348 4.1 45.0 1.0 CE2 A:PHE352 4.2 37.1 1.0 C15 A:K55922 4.2 32.5 1.0 CD1 A:LEU353 4.4 41.6 1.0 CD1 A:LEU255 4.5 40.6 1.0 CG2 A:VAL281 4.7 39.7 1.0 CB A:VAL281 4.8 39.4 1.0 C19 A:K55922 4.8 32.1 1.0 CD2 A:PHE352 4.9 39.5 1.0 CZ A:PHE352 5.0 37.8 1.0

Fluorine binding site 4 out of 8 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP204


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 TIPP204 within 5.0Å range: probe atom residue distance (Å) B Occ A:F922 b:34.2 occ:1.00 F32 A:K55922 0.0 34.2 1.0 C20 A:K55922 1.3 33.4 1.0 F30 A:K55922 2.1 34.4 1.0 F31 A:K55922 2.2 32.4 1.0 C17 A:K55922 2.4 33.2 1.0 C18 A:K55922 3.0 31.5 1.0 CD A:ARG284 3.2 44.7 1.0 C16 A:K55922 3.5 33.7 1.0 CB A:ARG284 3.7 40.4 1.0 CG A:ARG284 3.7 42.6 1.0 CD1 A:LEU255 3.9 40.6 1.0 NE A:ARG284 4.2 45.8 1.0 C19 A:K55922 4.3 32.1 1.0 CG1 A:VAL281 4.3 39.2 1.0 CA A:VAL281 4.4 38.2 1.0 C15 A:K55922 4.7 32.5 1.0 CB A:VAL281 4.7 39.4 1.0 CG2 A:VAL281 4.8 39.7 1.0 CG2 A:VAL348 4.8 45.0 1.0 O A:VAL281 4.9 36.5 1.0

Fluorine binding site 5 out of 8 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP204


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 TIPP204 within 5.0Å range: probe atom residue distance (Å) B Occ B:F923 b:25.5 occ:1.00 F29 B:K55923 0.0 25.5 1.0 C15 B:K55923 1.3 29.4 1.0 C16 B:K55923 2.4 29.1 1.0 C14 B:K55923 2.4 29.9 1.0 N27 B:K55923 2.9 35.2 1.0 C13 B:K55923 2.9 31.0 1.0 SG B:CYS285 3.4 38.5 1.0 CD2 B:LEU353 3.6 33.9 1.0 C19 B:K55923 3.7 30.3 1.0 C17 B:K55923 3.7 29.5 1.0 CD2 B:LEU339 3.7 34.3 1.0 CD1 B:LEU339 3.9 30.4 1.0 O28 B:K55923 3.9 29.8 1.0 C12 B:K55923 4.1 36.1 1.0 O33 B:K55923 4.1 37.7 1.0 C18 B:K55923 4.2 28.9 1.0 CD1 B:ILE364 4.2 33.0 1.0 CG B:LEU339 4.4 32.3 1.0 C22 B:K55923 4.4 37.4 1.0 CG B:LEU353 4.4 35.4 1.0 CD1 B:LEU353 4.6 33.2 1.0 C21 B:K55923 4.7 38.3 1.0 C8 B:K55923 4.7 38.5 1.0 C9 B:K55923 4.8 38.9 1.0 CG1 B:VAL281 4.8 26.2 1.0 C20 B:K55923 4.9 29.8 1.0

Fluorine binding site 6 out of 8 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP204


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 TIPP204 within 5.0Å range: probe atom residue distance (Å) B Occ B:F923 b:31.6 occ:1.00 F30 B:K55923 0.0 31.6 1.0 C20 B:K55923 1.3 29.8 1.0 F32 B:K55923 2.1 29.8 1.0 F31 B:K55923 2.1 31.7 1.0 C17 B:K55923 2.3 29.5 1.0 C18 B:K55923 3.0 28.9 1.0 CH2 B:TRP264 3.2 49.6 1.0 CG2 B:VAL348 3.3 35.3 1.0 C16 B:K55923 3.5 29.1 1.0 CZ2 B:TRP264 3.9 49.8 1.0 CG1 B:VAL341 4.1 38.9 1.0 CD1 B:ILE249 4.2 33.7 1.0 CZ3 B:TRP264 4.2 50.2 1.0 C19 B:K55923 4.3 30.3 1.0 CG1 B:VAL348 4.4 32.6 1.0 CG2 B:VAL341 4.5 38.9 1.0 CD1 B:LEU255 4.5 38.4 1.0 CB B:VAL348 4.5 34.1 1.0 CB B:VAL341 4.6 39.3 1.0 C15 B:K55923 4.6 29.4 1.0 CB B:ARG284 4.9 37.3 1.0 C14 B:K55923 5.0 29.9 1.0

Fluorine binding site 7 out of 8 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP204


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 TIPP204 within 5.0Å range: probe atom residue distance (Å) B Occ B:F923 b:31.7 occ:1.00 F31 B:K55923 0.0 31.7 1.0 C20 B:K55923 1.3 29.8 1.0 F30 B:K55923 2.1 31.6 1.0 F32 B:K55923 2.1 29.8 1.0 C17 B:K55923 2.4 29.5 1.0 C16 B:K55923 2.8 29.1 1.0 CG1 B:VAL348 3.6 32.6 1.0 C18 B:K55923 3.7 28.9 1.0 CG2 B:VAL348 3.8 35.3 1.0 CG1 B:VAL281 3.8 26.2 1.0 CG2 B:VAL281 4.0 26.6 1.0 C15 B:K55923 4.2 29.4 1.0 CD1 B:LEU353 4.2 33.2 1.0 CD1 B:LEU255 4.3 38.4 1.0 CB B:VAL348 4.3 34.1 1.0 CB B:VAL281 4.4 27.1 1.0 CE2 B:PHE352 4.7 37.5 1.0 CA B:VAL281 4.7 27.4 1.0 C19 B:K55923 4.8 30.3 1.0

Fluorine binding site 8 out of 8 in the Human Ppar Delta Ligand Binding Domain in Complex with A Synthetic Agonist TIPP204


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 TIPP204 within 5.0Å range: probe atom residue distance (Å) B Occ B:F923 b:29.8 occ:1.00 F32 B:K55923 0.0 29.8 1.0 C20 B:K55923 1.3 29.8 1.0 F30 B:K55923 2.1 31.6 1.0 F31 B:K55923 2.1 31.7 1.0 C17 B:K55923 2.4 29.5 1.0 C18 B:K55923 3.0 28.9 1.0 CB B:ARG284 3.2 37.3 1.0 CG B:ARG284 3.5 40.9 1.0 C16 B:K55923 3.5 29.1 1.0 CH2 B:TRP264 4.1 49.6 1.0 CA B:VAL281 4.2 27.4 1.0 CD1 B:LEU255 4.2 38.4 1.0 C19 B:K55923 4.3 30.3 1.0 CD B:ARG284 4.5 44.4 1.0 CG1 B:VAL281 4.5 26.2 1.0 CG2 B:VAL281 4.5 26.6 1.0 NH1 B:ARG284 4.5 49.0 1.0 CZ2 B:TRP264 4.5 49.8 1.0 CB B:VAL281 4.6 27.1 1.0 O B:VAL281 4.7 25.6 1.0 CA B:ARG284 4.7 35.4 1.0 C15 B:K55923 4.7 29.4 1.0 C B:VAL281 5.0 27.7 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