Fluorine in PDB 5u46: Human Ppardelta Ligand-Binding Domain in Complexed with GW501516

The structure of Human Ppardelta Ligand-Binding Domain in Complexed with GW501516, PDB code: 5u46 was solved by C.-C.Wu, T.J.Baiga, M.Downes, J.J.La Clair, A.R.Atkins, S.B.Richard, T.A.Stockley-Noel, M.E.Bowman, R.M.Evans, J.P.Noel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.90 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.860, 94.140, 96.470, 90.00, 96.77, 90.00
R / Rfree (%)	17.4 / 22.1

The binding sites of Fluorine atom in the Human Ppardelta Ligand-Binding Domain in Complexed with GW501516 (pdb code 5u46). 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 Ppardelta Ligand-Binding Domain in Complexed with GW501516, PDB code: 5u46:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Human Ppardelta Ligand-Binding Domain in Complexed with GW501516


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Ppardelta Ligand-Binding Domain in Complexed with GW501516 within 5.0Å range: probe atom residue distance (Å) B Occ A:F505 b:62.9 occ:1.00 F A:7T1505 0.0 62.9 1.0 C6 A:7T1505 1.3 54.4 1.0 F2 A:7T1505 2.1 55.1 1.0 F1 A:7T1505 2.2 60.6 1.0 C2 A:7T1505 2.3 42.2 1.0 H1 A:7T1505 2.4 43.9 1.0 HG21 A:VAL312 2.5 38.5 0.5 C1 A:7T1505 2.7 36.5 1.0 HG11 A:VAL312 2.8 38.4 0.5 HG21 A:VAL312 2.8 40.2 0.5 CG2 A:VAL312 3.3 32.1 0.5 HG22 A:VAL312 3.3 38.5 0.5 HB A:VAL312 3.4 37.1 0.5 CG1 A:VAL312 3.5 32.0 0.5 HG11 A:VAL312 3.6 30.6 0.5 CG2 A:VAL312 3.6 33.5 0.5 HG13 A:VAL312 3.6 38.4 0.5 C3 A:7T1505 3.6 44.8 1.0 HG22 A:VAL245 3.6 42.3 1.0 HG13 A:VAL245 3.6 43.4 1.0 HD13 A:LEU219 3.7 43.0 1.0 HG23 A:VAL312 3.7 40.2 0.5 HE2 A:PHE316 3.8 45.1 1.0 CB A:VAL312 3.9 30.9 0.5 HD21 A:LEU317 3.9 37.0 1.0 H2 A:7T1505 3.9 53.8 1.0 CB A:VAL312 3.9 30.5 0.5 HG11 A:VAL305 4.0 29.8 1.0 HG23 A:VAL312 4.0 38.5 0.5 C A:7T1505 4.1 38.9 1.0 HD11 A:LEU219 4.2 43.0 1.0 CG1 A:VAL312 4.2 25.5 0.5 HG21 A:ILE213 4.2 33.7 1.0 HB A:VAL312 4.2 36.6 0.5 HG12 A:VAL312 4.3 38.4 0.5 HG22 A:VAL312 4.4 40.2 0.5 CD1 A:LEU219 4.4 35.8 1.0 CG2 A:VAL245 4.5 35.3 1.0 HH2 A:TRP228 4.5 35.8 1.0 HD13 A:ILE213 4.5 36.7 1.0 CG1 A:VAL245 4.5 36.1 1.0 HA A:VAL245 4.5 25.0 1.0 CE2 A:PHE316 4.7 37.6 1.0 HG21 A:VAL245 4.7 42.3 1.0 HG21 A:VAL305 4.7 29.9 1.0 HG11 A:VAL245 4.7 43.4 1.0 HG12 A:VAL312 4.7 30.6 0.5 C4 A:7T1505 4.7 47.8 1.0 HD12 A:ILE213 4.7 36.7 1.0 H A:7T1505 4.8 46.7 1.0 HB3 A:ARG248 4.8 40.9 1.0 HG3 A:ARG248 4.8 45.7 1.0 CD2 A:LEU317 4.8 30.9 1.0 HD22 A:LEU219 4.8 55.3 1.0 HD2 A:PHE316 4.8 46.0 1.0 HB2 A:ARG248 4.8 40.9 1.0 HD23 A:LEU317 4.9 37.0 1.0 HD12 A:LEU219 4.9 43.0 1.0 HG13 A:VAL312 4.9 30.6 0.5 CG1 A:VAL305 4.9 24.8 1.0 C5 A:7T1505 4.9 45.9 1.0 CB A:VAL245 5.0 22.6 1.0 HB A:ILE213 5.0 31.4 1.0 HG22 A:ILE213 5.0 33.7 1.0

Fluorine binding site 2 out of 6 in the Human Ppardelta Ligand-Binding Domain in Complexed with GW501516


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Ppardelta Ligand-Binding Domain in Complexed with GW501516 within 5.0Å range: probe atom residue distance (Å) B Occ A:F505 b:60.6 occ:1.00 F1 A:7T1505 0.0 60.6 1.0 C6 A:7T1505 1.3 54.4 1.0 F2 A:7T1505 2.1 55.1 1.0 F A:7T1505 2.2 62.9 1.0 C2 A:7T1505 2.3 42.2 1.0 H2 A:7T1505 2.5 53.8 1.0 HH2 A:TRP228 2.6 35.8 1.0 HG21 A:VAL312 2.7 38.5 0.5 C3 A:7T1505 2.8 44.8 1.0 HG11 A:VAL305 2.8 29.8 1.0 HG21 A:VAL305 3.2 29.9 1.0 HZ3 A:TRP228 3.3 39.4 1.0 CH2 A:TRP228 3.4 29.8 1.0 CG2 A:VAL312 3.5 32.1 0.5 C1 A:7T1505 3.5 36.5 1.0 HG22 A:VAL312 3.6 38.5 0.5 CG1 A:VAL305 3.7 24.8 1.0 CZ3 A:TRP228 3.7 32.8 1.0 HB A:VAL305 3.7 32.9 1.0 HG23 A:VAL312 3.7 38.5 0.5 H1 A:7T1505 3.8 43.9 1.0 HB A:VAL312 3.9 37.1 0.5 HB3 A:ARG248 3.9 40.9 1.0 CG2 A:VAL305 4.0 24.9 1.0 CB A:VAL305 4.0 27.4 1.0 HD2 A:ARG248 4.1 46.1 1.0 C4 A:7T1505 4.1 47.8 1.0 HD13 A:ILE213 4.1 36.7 1.0 HG12 A:VAL305 4.1 29.8 1.0 HG3 A:ARG248 4.1 45.7 1.0 HD11 A:LEU219 4.1 43.0 1.0 HD12 A:ILE213 4.2 36.7 1.0 HG11 A:VAL312 4.2 30.6 0.5 HD13 A:LEU219 4.2 43.0 1.0 HG13 A:VAL305 4.3 29.8 1.0 HG11 A:VAL312 4.4 38.4 0.5 HG21 A:VAL312 4.5 40.2 0.5 CZ2 A:TRP228 4.5 37.4 1.0 CD1 A:ILE213 4.6 30.6 1.0 CD1 A:LEU219 4.6 35.8 1.0 HG23 A:VAL305 4.6 29.9 1.0 CB A:ARG248 4.6 34.1 1.0 HG22 A:VAL305 4.6 29.9 1.0 C A:7T1505 4.7 38.9 1.0 HB2 A:ARG248 4.7 40.9 1.0 CB A:VAL312 4.7 30.9 0.5 CG A:ARG248 4.7 38.1 1.0 CB A:VAL312 4.7 30.5 0.5 HZ2 A:TRP228 4.7 44.8 1.0 H3 A:7T1505 4.8 57.4 1.0 CG1 A:VAL312 4.8 25.5 0.5 HD12 A:LEU219 4.8 43.0 1.0 CD A:ARG248 4.8 38.4 1.0 HG12 A:VAL312 4.8 30.6 0.5 C5 A:7T1505 4.9 45.9 1.0 HG21 A:ILE213 4.9 33.7 1.0 HB A:VAL312 4.9 36.6 0.5 CG1 A:VAL312 4.9 32.0 0.5 HD11 A:ILE213 5.0 36.7 1.0

Fluorine binding site 3 out of 6 in the Human Ppardelta Ligand-Binding Domain in Complexed with GW501516


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Ppardelta Ligand-Binding Domain in Complexed with GW501516 within 5.0Å range: probe atom residue distance (Å) B Occ A:F505 b:55.1 occ:1.00 F2 A:7T1505 0.0 55.1 1.0 C6 A:7T1505 1.3 54.4 1.0 F1 A:7T1505 2.1 60.6 1.0 F A:7T1505 2.1 62.9 1.0 C2 A:7T1505 2.3 42.2 1.0 HG3 A:ARG248 2.7 45.7 1.0 HB3 A:ARG248 2.9 40.9 1.0 HB2 A:ARG248 2.9 40.9 1.0 C3 A:7T1505 3.1 44.8 1.0 H2 A:7T1505 3.1 53.8 1.0 CB A:ARG248 3.2 34.1 1.0 C1 A:7T1505 3.3 36.5 1.0 HA A:VAL245 3.3 25.0 1.0 CG A:ARG248 3.3 38.1 1.0 H1 A:7T1505 3.4 43.9 1.0 HG22 A:VAL245 3.5 42.3 1.0 HG13 A:VAL245 3.5 43.4 1.0 HD11 A:LEU219 3.7 43.0 1.0 HD2 A:ARG248 3.7 46.1 1.0 HD13 A:LEU219 4.1 43.0 1.0 HG2 A:ARG248 4.1 45.7 1.0 CD A:ARG248 4.1 38.4 1.0 HH2 A:TRP228 4.1 35.8 1.0 HG21 A:VAL312 4.2 38.5 0.5 CA A:VAL245 4.2 20.9 1.0 C4 A:7T1505 4.3 47.8 1.0 CD1 A:LEU219 4.4 35.8 1.0 CG2 A:VAL245 4.4 35.3 1.0 CG1 A:VAL245 4.4 36.1 1.0 C A:7T1505 4.5 38.9 1.0 HD21 A:LEU219 4.5 55.3 1.0 HZ3 A:TRP228 4.6 39.4 1.0 CB A:VAL245 4.6 22.6 1.0 O A:VAL245 4.6 27.6 1.0 CA A:ARG248 4.7 31.1 1.0 CH2 A:TRP228 4.7 29.8 1.0 HG11 A:VAL305 4.7 29.8 1.0 HD2 A:HIS244 4.8 29.3 1.0 HD3 A:ARG248 4.8 46.1 1.0 HE A:ARG248 4.8 55.2 1.0 HG11 A:VAL312 4.9 38.4 0.5 CZ3 A:TRP228 4.9 32.8 1.0 C5 A:7T1505 4.9 45.9 1.0 HD22 A:LEU219 4.9 55.3 1.0 HG23 A:VAL245 4.9 42.3 1.0 C A:VAL245 4.9 20.1 1.0 HG21 A:VAL312 4.9 40.2 0.5 HG12 A:VAL245 4.9 43.4 1.0 HD12 A:LEU219 4.9 43.0 1.0 NE A:ARG248 5.0 46.0 1.0 HG21 A:VAL245 5.0 42.3 1.0

Fluorine binding site 4 out of 6 in the Human Ppardelta Ligand-Binding Domain in Complexed with GW501516


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Ppardelta Ligand-Binding Domain in Complexed with GW501516 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:61.8 occ:1.00 F B:7T1502 0.0 61.8 1.0 C6 B:7T1502 1.3 48.1 1.0 F2 B:7T1502 2.1 55.0 1.0 F1 B:7T1502 2.2 48.0 1.0 C2 B:7T1502 2.3 28.5 1.0 H1 B:7T1502 2.4 35.9 1.0 HG21 B:VAL312 2.4 29.7 0.4 C1 B:7T1502 2.7 29.9 1.0 HG21 B:VAL312 2.7 29.7 0.6 HG11 B:VAL312 2.8 26.8 0.4 CG2 B:VAL312 3.2 24.7 0.4 HG22 B:VAL312 3.2 29.7 0.4 HB B:VAL312 3.4 24.0 0.6 HD13 B:LEU219 3.5 72.1 1.0 CG2 B:VAL312 3.5 24.8 0.6 HG13 B:VAL245 3.5 27.0 1.0 CG1 B:VAL312 3.5 22.3 0.4 HG13 B:VAL312 3.5 26.8 0.4 HG22 B:VAL245 3.6 28.4 1.0 HG11 B:VAL312 3.6 23.4 0.6 HD11 B:LEU219 3.6 72.1 1.0 C3 B:7T1502 3.6 32.6 1.0 HG23 B:VAL312 3.7 29.7 0.6 HD21 B:LEU317 3.7 18.7 1.0 HE2 B:PHE316 3.8 31.9 1.0 CB B:VAL312 3.8 20.0 0.6 CD1 B:LEU219 3.9 60.1 1.0 CB B:VAL312 3.9 20.6 0.4 H2 B:7T1502 4.0 39.1 1.0 HG23 B:VAL312 4.0 29.7 0.4 HG11 B:VAL305 4.0 34.9 1.0 HG21 B:ILE213 4.1 23.4 1.0 C B:7T1502 4.1 40.3 1.0 HD12 B:LEU219 4.2 72.1 1.0 CG1 B:VAL312 4.2 19.5 0.6 HB B:VAL312 4.3 24.7 0.4 HG22 B:VAL312 4.3 29.7 0.6 CG1 B:VAL245 4.4 22.5 1.0 HG12 B:VAL312 4.4 26.8 0.4 CG2 B:VAL245 4.4 23.7 1.0 HG11 B:VAL245 4.5 27.0 1.0 HD13 B:ILE213 4.5 30.2 1.0 HG21 B:VAL245 4.5 28.4 1.0 CD2 B:LEU317 4.6 15.6 1.0 CE2 B:PHE316 4.6 26.6 1.0 HH2 B:TRP228 4.6 31.9 1.0 HA B:VAL245 4.7 23.9 1.0 HG21 B:VAL305 4.7 25.3 1.0 HD23 B:LEU317 4.7 18.7 1.0 HG12 B:VAL312 4.7 23.4 0.6 C4 B:7T1502 4.7 34.5 1.0 HD2 B:PHE316 4.7 32.3 1.0 H B:7T1502 4.7 48.4 1.0 HG22 B:ILE213 4.8 23.4 1.0 CG2 B:ILE213 4.9 19.5 1.0 HG13 B:VAL312 4.9 23.4 0.6 HD12 B:ILE213 4.9 30.2 1.0 CB B:VAL245 4.9 26.9 1.0 C5 B:7T1502 4.9 36.6 1.0 HB2 B:ARG248 4.9 33.5 1.0 CG1 B:VAL305 4.9 29.1 1.0 HG3 B:ARG248 5.0 34.7 1.0 HD22 B:LEU317 5.0 18.7 1.0 HB3 B:ARG248 5.0 33.5 1.0

Fluorine binding site 5 out of 6 in the Human Ppardelta Ligand-Binding Domain in Complexed with GW501516


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Ppardelta Ligand-Binding Domain in Complexed with GW501516 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:48.0 occ:1.00 F1 B:7T1502 0.0 48.0 1.0 C6 B:7T1502 1.3 48.1 1.0 F2 B:7T1502 2.1 55.0 1.0 F B:7T1502 2.2 61.8 1.0 C2 B:7T1502 2.3 28.5 1.0 H2 B:7T1502 2.6 39.1 1.0 HG21 B:VAL312 2.7 29.7 0.4 HH2 B:TRP228 2.8 31.9 1.0 C3 B:7T1502 2.8 32.6 1.0 HG11 B:VAL305 2.9 34.9 1.0 HG21 B:VAL305 3.3 25.3 1.0 HZ3 B:TRP228 3.5 33.1 1.0 CG2 B:VAL312 3.5 24.7 0.4 C1 B:7T1502 3.5 29.9 1.0 CH2 B:TRP228 3.5 26.6 1.0 HG22 B:VAL312 3.6 29.7 0.4 HD11 B:LEU219 3.7 72.1 1.0 HG23 B:VAL312 3.7 29.7 0.4 CG1 B:VAL305 3.8 29.1 1.0 H1 B:7T1502 3.8 35.9 1.0 HB B:VAL305 3.8 31.7 1.0 CZ3 B:TRP228 3.9 27.6 1.0 HB B:VAL312 3.9 24.0 0.6 HB3 B:ARG248 4.0 33.5 1.0 HD13 B:ILE213 4.0 30.2 1.0 HG3 B:ARG248 4.1 34.7 1.0 CG2 B:VAL305 4.1 21.1 1.0 CB B:VAL305 4.1 26.4 1.0 C4 B:7T1502 4.1 34.5 1.0 HG12 B:VAL305 4.2 34.9 1.0 HG11 B:VAL312 4.2 23.4 0.6 HD12 B:LEU219 4.3 72.1 1.0 CD1 B:LEU219 4.3 60.1 1.0 HD13 B:LEU219 4.3 72.1 1.0 HD12 B:ILE213 4.4 30.2 1.0 HD2 B:ARG248 4.4 43.7 1.0 HG13 B:VAL305 4.4 34.9 1.0 HG21 B:VAL312 4.4 29.7 0.6 HG11 B:VAL312 4.4 26.8 0.4 HB2 B:ARG248 4.6 33.5 1.0 CB B:ARG248 4.6 27.9 1.0 CZ2 B:TRP228 4.6 27.9 1.0 C B:7T1502 4.6 40.3 1.0 CD1 B:ILE213 4.7 25.2 1.0 CB B:VAL312 4.7 20.0 0.6 HG23 B:VAL305 4.7 25.3 1.0 CG B:ARG248 4.7 28.9 1.0 HG22 B:VAL305 4.7 25.3 1.0 CB B:VAL312 4.7 20.6 0.4 HG21 B:ILE213 4.7 23.4 1.0 CG1 B:VAL312 4.8 19.5 0.6 H3 B:7T1502 4.8 41.4 1.0 HZ2 B:TRP228 4.8 33.5 1.0 HG13 B:VAL245 4.8 27.0 1.0 HG12 B:VAL312 4.9 23.4 0.6 C5 B:7T1502 4.9 36.6 1.0 HB B:VAL312 5.0 24.7 0.4 CG1 B:VAL312 5.0 22.3 0.4 CG2 B:VAL312 5.0 24.8 0.6

Fluorine binding site 6 out of 6 in the Human Ppardelta Ligand-Binding Domain in Complexed with GW501516


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Ppardelta Ligand-Binding Domain in Complexed with GW501516 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:55.0 occ:1.00 F2 B:7T1502 0.0 55.0 1.0 C6 B:7T1502 1.3 48.1 1.0 F1 B:7T1502 2.1 48.0 1.0 F B:7T1502 2.1 61.8 1.0 C2 B:7T1502 2.3 28.5 1.0 HG3 B:ARG248 2.9 34.7 1.0 HB2 B:ARG248 2.9 33.5 1.0 C3 B:7T1502 3.0 32.6 1.0 H2 B:7T1502 3.1 39.1 1.0 HB3 B:ARG248 3.1 33.5 1.0 HG22 B:VAL245 3.2 28.4 1.0 HA B:VAL245 3.2 23.9 1.0 HG13 B:VAL245 3.2 27.0 1.0 C1 B:7T1502 3.3 29.9 1.0 HD11 B:LEU219 3.3 72.1 1.0 CB B:ARG248 3.4 27.9 1.0 H1 B:7T1502 3.4 35.9 1.0 CG B:ARG248 3.6 28.9 1.0 HD13 B:LEU219 4.0 72.1 1.0 CD1 B:LEU219 4.0 60.1 1.0 CA B:VAL245 4.1 20.0 1.0 CG2 B:VAL245 4.1 23.7 1.0 CG1 B:VAL245 4.1 22.5 1.0 HG21 B:VAL312 4.2 29.7 0.4 HD2 B:ARG248 4.2 43.7 1.0 HG2 B:ARG248 4.2 34.7 1.0 C4 B:7T1502 4.3 34.5 1.0 CB B:VAL245 4.3 26.9 1.0 HH2 B:TRP228 4.3 31.9 1.0 C B:7T1502 4.5 40.3 1.0 HD12 B:LEU219 4.5 72.1 1.0 CD B:ARG248 4.5 36.4 1.0 O B:VAL245 4.6 25.5 1.0 HD21 B:LEU219 4.6 54.2 1.0 HG21 B:VAL245 4.6 28.4 1.0 HG11 B:VAL245 4.6 27.0 1.0 HG23 B:VAL245 4.6 28.4 1.0 HD2 B:HIS244 4.7 22.1 1.0 HG12 B:VAL245 4.7 27.0 1.0 HZ3 B:TRP228 4.7 33.1 1.0 HG11 B:VAL305 4.7 34.9 1.0 CA B:ARG248 4.8 24.5 1.0 HG21 B:VAL312 4.8 29.7 0.6 C B:VAL245 4.9 25.4 1.0 CH2 B:TRP228 4.9 26.6 1.0 C5 B:7T1502 4.9 36.6 1.0 HG11 B:VAL312 4.9 26.8 0.4

C.C.Wu, T.J.Baiga, M.Downes, J.J.La Clair, A.R.Atkins, S.B.Richard, W.Fan, T.A.Stockley-Noel, M.E.Bowman, J.P.Noel, R.M.Evans. Structural Basis For Specific Ligation of the Peroxisome Proliferator-Activated Receptor Delta. Proc. Natl. Acad. Sci. V. 114 E2563 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28320959
DOI: 10.1073/PNAS.1621513114