Fluorine in PDB 8zfp: Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and MRL24

The structure of Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and MRL24, PDB code: 8zfp was solved by J.Shang, D.J.Kojetin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.13 / 2.48
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	91.844, 62.221, 119.237, 90, 102.28, 90
R / Rfree (%)	23.7 / 30.3

The binding sites of Fluorine atom in the Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and MRL24 (pdb code 8zfp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and MRL24, PDB code: 8zfp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and MRL24


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and MRL24 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:30.0 occ:1.00 FAI A:241502 0.0 30.0 1.0 CBL A:241502 1.3 30.0 1.0 FAG A:241502 2.2 30.0 1.0 FAH A:241502 2.2 30.0 1.0 OAX A:241502 2.2 30.0 1.0 CBE A:241502 2.9 30.0 1.0 CAT A:241502 3.1 30.0 1.0 O1 A:GW9501 3.4 66.4 1.0 SD A:MET364 3.6 62.4 1.0 CAQ A:241502 4.1 30.0 1.0 CE A:LYS367 4.1 52.8 1.0 CB A:CYS285 4.1 52.1 1.0 CD2 A:LEU330 4.2 33.0 1.0 SG A:CYS285 4.2 58.6 1.0 C1 A:GW9501 4.2 66.4 1.0 CD A:LYS367 4.3 49.0 1.0 CBH A:241502 4.3 30.0 1.0 CE1 A:TYR327 4.4 46.9 1.0 CE A:MET364 4.5 53.2 1.0 C9 A:GW9501 4.6 62.5 1.0 C3 A:GW9501 4.7 66.8 1.0 C8 A:GW9501 4.8 62.2 1.0 CE1 A:HIS449 4.9 61.0 1.0 OG A:SER289 4.9 52.5 1.0 CG A:LYS367 4.9 47.0 1.0 CD1 A:TYR327 5.0 40.6 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and MRL24


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and MRL24 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:30.0 occ:1.00 FAG A:241502 0.0 30.0 1.0 CBL A:241502 1.3 30.0 1.0 FAH A:241502 2.2 30.0 1.0 FAI A:241502 2.2 30.0 1.0 OAX A:241502 2.2 30.0 1.0 CE1 A:HIS449 3.4 61.0 1.0 O1 A:GW9501 3.4 66.4 1.0 C3 A:GW9501 3.5 66.8 1.0 CBE A:241502 3.5 30.0 1.0 OG A:SER289 3.6 52.5 1.0 CE1 A:TYR327 3.7 46.9 1.0 ND1 A:HIS449 3.9 63.8 1.0 C4 A:GW9501 3.9 65.8 1.0 OH A:TYR327 4.1 59.9 1.0 NE2 A:HIS449 4.3 63.2 1.0 C1 A:GW9501 4.3 66.4 1.0 CAQ A:241502 4.3 30.0 1.0 CAT A:241502 4.4 30.0 1.0 CE A:LYS367 4.4 52.8 1.0 CZ A:TYR327 4.4 54.7 1.0 C2 A:GW9501 4.5 67.3 1.0 CB A:CYS285 4.7 52.1 1.0 CD1 A:TYR327 4.7 40.6 1.0 N1 A:GW9501 4.8 67.0 1.0 CG2 A:ILE326 4.9 35.3 1.0 CB A:SER289 5.0 49.3 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and MRL24


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and MRL24 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:30.0 occ:1.00 FAH A:241502 0.0 30.0 1.0 CBL A:241502 1.3 30.0 1.0 FAG A:241502 2.2 30.0 1.0 FAI A:241502 2.2 30.0 1.0 OAX A:241502 2.2 30.0 1.0 CBE A:241502 2.7 30.0 1.0 CE1 A:TYR327 3.2 46.9 1.0 CAQ A:241502 3.2 30.0 1.0 CG2 A:ILE326 3.3 35.3 1.0 CAT A:241502 3.6 30.0 1.0 CD1 A:TYR327 3.6 40.6 1.0 CD2 A:LEU330 4.0 33.0 1.0 OG A:SER289 4.0 52.5 1.0 CAR A:241502 4.3 30.0 1.0 CZ A:TYR327 4.4 54.7 1.0 CBH A:241502 4.6 30.0 1.0 OH A:TYR327 4.7 59.9 1.0 CB A:ILE326 4.7 38.0 1.0 CE A:LYS367 4.8 52.8 1.0 CBI A:241502 4.9 30.0 1.0 CG A:LEU330 4.9 34.0 1.0 CG A:TYR327 5.0 41.0 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and MRL24


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and MRL24 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:30.0 occ:1.00 FAI B:241502 0.0 30.0 1.0 CBL B:241502 1.3 30.0 1.0 FAH B:241502 2.2 30.0 1.0 FAG B:241502 2.2 30.0 1.0 OAX B:241502 2.2 30.0 1.0 CE1 B:TYR327 2.7 54.5 1.0 CBE B:241502 2.9 30.0 1.0 CD1 B:TYR327 3.3 53.1 1.0 CG2 B:ILE326 3.3 36.9 1.0 CAQ B:241502 3.4 30.0 1.0 CAT B:241502 3.7 30.0 1.0 CZ B:TYR327 3.9 59.6 1.0 OH B:TYR327 4.2 66.9 1.0 CD2 B:LEU330 4.3 46.1 1.0 OG B:SER289 4.5 53.7 1.0 CAR B:241502 4.5 30.0 1.0 O1 B:GW9501 4.5 66.5 1.0 CB B:ILE326 4.6 35.8 1.0 CG B:TYR327 4.6 49.2 1.0 CE B:LYS367 4.7 54.7 1.0 CBH B:241502 4.8 30.0 1.0 C3 B:GW9501 4.8 57.4 1.0 C4 B:GW9501 4.9 64.1 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and MRL24


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and MRL24 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:30.0 occ:1.00 FAG B:241502 0.0 30.0 1.0 CBL B:241502 1.3 30.0 1.0 FAH B:241502 2.2 30.0 1.0 FAI B:241502 2.2 30.0 1.0 OAX B:241502 2.2 30.0 1.0 CBE B:241502 2.8 30.0 1.0 CAT B:241502 2.9 30.0 1.0 O1 B:GW9501 3.0 66.5 1.0 CD2 B:LEU330 3.9 46.1 1.0 CAQ B:241502 4.0 30.0 1.0 CE B:MET364 4.0 44.1 1.0 CE B:LYS367 4.1 54.7 1.0 C1 B:GW9501 4.1 64.4 1.0 CBH B:241502 4.1 30.0 1.0 SG B:CYS285 4.2 68.3 1.0 CE1 B:TYR327 4.3 54.5 1.0 SD B:MET364 4.3 74.7 1.0 CD B:LYS367 4.4 60.9 1.0 C3 B:GW9501 4.5 57.4 1.0 C9 B:GW9501 4.7 65.7 1.0 CG B:LYS367 4.7 53.4 1.0 C8 B:GW9501 4.8 66.8 1.0 CD1 B:TYR327 4.8 53.1 1.0 CB B:CYS285 4.9 60.3 1.0 CG B:MET364 5.0 59.4 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and MRL24


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and MRL24 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:30.0 occ:1.00 FAH B:241502 0.0 30.0 1.0 CBL B:241502 1.3 30.0 1.0 FAI B:241502 2.2 30.0 1.0 FAG B:241502 2.2 30.0 1.0 OAX B:241502 2.2 30.0 1.0 O1 B:GW9501 2.8 66.5 1.0 C3 B:GW9501 3.0 57.4 1.0 C4 B:GW9501 3.3 64.1 1.0 CE1 B:HIS449 3.3 67.8 1.0 CBE B:241502 3.5 30.0 1.0 ND1 B:HIS449 3.7 64.0 1.0 CE1 B:TYR327 3.8 54.5 1.0 OH B:TYR327 3.9 66.9 1.0 C1 B:GW9501 3.9 64.4 1.0 C2 B:GW9501 4.0 59.3 1.0 OG B:SER289 4.2 53.7 1.0 CAT B:241502 4.3 30.0 1.0 CZ B:TYR327 4.3 59.6 1.0 CE B:LYS367 4.3 54.7 1.0 NE2 B:HIS449 4.3 71.6 1.0 C5 B:GW9501 4.4 63.5 1.0 N1 B:GW9501 4.4 59.5 1.0 CAQ B:241502 4.5 30.0 1.0 CD1 B:TYR327 4.8 53.1 1.0 CE1 B:PHE363 4.8 71.4 1.0 CG B:HIS449 4.9 64.4 1.0 O B:HOH607 5.0 65.6 1.0 C7 B:GW9501 5.0 60.6 1.0

J.Shang, D.J.Kojetin. Unanticipated Mechanisms of Covalent Inhibitor and Synthetic Ligand Cobinding to Ppar Gamma. Elife 2024.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.99782.1