Fluorine in PDB 9dl7: Structure of Proline Utilization A Complexed with 1-(4-Fluorophenyl) Thiourea

All present enzymatic activity of Structure of Proline Utilization A Complexed with 1-(4-Fluorophenyl) Thiourea:
1.2.1.88; 1.5.5.2;

The structure of Structure of Proline Utilization A Complexed with 1-(4-Fluorophenyl) Thiourea, PDB code: 9dl7 was solved by J.J.Tanner, K.R.Meeks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.97 / 1.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	101.135, 101.867, 126.557, 90, 106.38, 90
R / Rfree (%)	20.8 / 24

The binding sites of Fluorine atom in the Structure of Proline Utilization A Complexed with 1-(4-Fluorophenyl) Thiourea (pdb code 9dl7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of Proline Utilization A Complexed with 1-(4-Fluorophenyl) Thiourea, PDB code: 9dl7:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Structure of Proline Utilization A Complexed with 1-(4-Fluorophenyl) Thiourea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Proline Utilization A Complexed with 1-(4-Fluorophenyl) Thiourea within 5.0Å range: probe atom residue distance (Å) B Occ A:F2005 b:37.3 occ:0.49 F1 A:8P42005 0.0 37.3 0.5 N2 A:8P42005 0.7 35.6 0.4 C7 A:8P42005 1.3 35.4 0.4 C3 A:8P42005 1.4 35.4 0.5 S1 A:8P42005 2.1 43.1 0.4 C2 A:8P42005 2.3 38.7 0.5 C4 A:8P42005 2.4 36.0 0.5 N1 A:8P42005 2.7 36.0 0.4 O A:HOH2344 2.9 36.6 1.0 C1 A:8P42005 3.6 35.0 0.5 C5 A:8P42005 3.7 35.3 0.5 CG A:GLN793 3.9 40.1 1.0 CA A:ALA767 3.9 31.4 1.0 CG1 A:ILE790 3.9 27.4 1.0 CB A:ALA767 4.0 30.6 1.0 C6 A:8P42005 4.0 35.8 0.4 C6 A:8P42005 4.1 36.8 0.5 O A:LEU789 4.2 28.1 1.0 CA A:ILE790 4.2 26.8 1.0 C1 A:8P42005 4.4 36.6 0.4 N A:ILE790 4.4 25.2 1.0 C A:LEU789 4.4 27.5 1.0 CB A:VAL770 4.5 29.0 1.0 CG1 A:VAL770 4.5 30.4 1.0 CB A:GLN793 4.6 35.2 1.0 N A:ALA767 4.7 31.9 1.0 CB A:ILE790 4.7 25.8 1.0 CG2 A:VAL770 4.8 28.7 1.0 CB A:LEU789 4.8 31.1 1.0 O A:ALA767 4.9 32.0 1.0 C A:ALA767 4.9 33.3 1.0

Fluorine binding site 2 out of 4 in the Structure of Proline Utilization A Complexed with 1-(4-Fluorophenyl) Thiourea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Proline Utilization A Complexed with 1-(4-Fluorophenyl) Thiourea within 5.0Å range: probe atom residue distance (Å) B Occ A:F2005 b:40.3 occ:0.41 F1 A:8P42005 0.0 40.3 0.4 N2 A:8P42005 0.3 40.1 0.5 C3 A:8P42005 1.4 38.0 0.4 C7 A:8P42005 1.4 38.5 0.5 C2 A:8P42005 2.3 36.8 0.4 N1 A:8P42005 2.4 36.8 0.5 C4 A:8P42005 2.4 36.3 0.4 S1 A:8P42005 2.6 35.9 0.5 O A:HOH2183 2.7 43.3 1.0 C1 A:8P42005 3.6 36.6 0.4 C5 A:8P42005 3.7 34.0 0.4 O A:HOH2725 3.7 37.0 1.0 C6 A:8P42005 3.8 36.8 0.5 CA A:GLY763 3.9 35.5 1.0 C6 A:8P42005 4.2 35.8 0.4 N A:GLY763 4.3 38.6 1.0 C1 A:8P42005 4.6 35.0 0.5 CG1 A:VAL786 4.6 29.2 1.0 C5 A:8P42005 4.7 35.3 0.5 CG2 A:VAL786 4.8 39.4 1.0 O A:HOH2194 4.9 38.3 1.0 O A:HOH2324 4.9 36.7 1.0 O A:HOH2728 5.0 38.3 1.0

Fluorine binding site 3 out of 4 in the Structure of Proline Utilization A Complexed with 1-(4-Fluorophenyl) Thiourea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Proline Utilization A Complexed with 1-(4-Fluorophenyl) Thiourea within 5.0Å range: probe atom residue distance (Å) B Occ B:F2005 b:36.1 occ:0.50 F1 B:8P42005 0.0 36.1 0.5 F1 B:8P42005 0.9 33.1 0.4 C3 B:8P42005 1.4 33.9 0.5 C3 B:8P42005 1.6 33.9 0.4 O B:HOH2582 2.1 34.9 1.0 C2 B:8P42005 2.3 32.8 0.5 C4 B:8P42005 2.4 31.9 0.5 C4 B:8P42005 2.5 32.3 0.4 C2 B:8P42005 2.5 30.4 0.4 O B:HOH2579 2.8 31.5 1.0 NZ B:LYS730 3.5 27.3 1.0 C1 B:8P42005 3.6 33.5 0.5 C5 B:8P42005 3.7 31.9 0.5 C5 B:8P42005 3.7 32.6 0.4 C1 B:8P42005 3.7 31.2 0.4 O B:HOH2290 3.8 30.9 1.0 O B:HOH2568 3.9 35.4 1.0 C6 B:8P42005 4.1 32.2 0.5 C6 B:8P42005 4.2 32.0 0.4 CE B:LYS730 4.2 24.1 1.0 CG2 B:ILE703 4.3 21.0 1.0 O B:HOH2344 4.6 38.8 1.0 O B:HOH2734 4.6 33.2 1.0 CA B:ALA732 4.7 20.9 1.0 O B:SER704 4.9 21.4 1.0 CA B:GLY763 4.9 30.0 1.0 N B:GLY763 5.0 29.9 1.0

Fluorine binding site 4 out of 4 in the Structure of Proline Utilization A Complexed with 1-(4-Fluorophenyl) Thiourea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Proline Utilization A Complexed with 1-(4-Fluorophenyl) Thiourea within 5.0Å range: probe atom residue distance (Å) B Occ B:F2005 b:33.1 occ:0.40 F1 B:8P42005 0.0 33.1 0.4 F1 B:8P42005 0.9 36.1 0.5 C3 B:8P42005 1.4 33.9 0.4 C3 B:8P42005 1.5 33.9 0.5 C2 B:8P42005 2.3 30.4 0.4 O B:HOH2579 2.3 31.5 1.0 C2 B:8P42005 2.4 32.8 0.5 C4 B:8P42005 2.4 31.9 0.5 C4 B:8P42005 2.4 32.3 0.4 O B:HOH2582 2.6 34.9 1.0 NZ B:LYS730 2.9 27.3 1.0 C1 B:8P42005 3.6 33.5 0.5 C5 B:8P42005 3.6 31.9 0.5 C1 B:8P42005 3.6 31.2 0.4 C5 B:8P42005 3.7 32.6 0.4 CE B:LYS730 3.8 24.1 1.0 C6 B:8P42005 4.0 32.2 0.5 O B:HOH2344 4.1 38.8 1.0 O B:HOH2290 4.1 30.9 1.0 N B:GLY763 4.1 29.9 1.0 C6 B:8P42005 4.1 32.0 0.4 CA B:GLY763 4.2 30.0 1.0 C B:ASP762 4.3 32.1 1.0 O B:ASP762 4.5 28.8 1.0 CA B:ALA732 4.7 20.9 1.0 N B:GLU733 4.8 23.1 1.0 CG2 B:ILE703 4.8 21.0 1.0 CA B:ASP762 4.8 33.3 1.0 O B:HOH2568 4.8 35.4 1.0 O B:GLY761 4.8 26.5 1.0 O B:PRO731 4.9 21.6 1.0

K.R.Meeks, A.N.Bogner, J.C.Nix, J.J.Tanner. Crystallographic Fragment Screening of A Bifunctional Proline Catabolic Enzyme Reveals New Inhibitor Templates For Proline Dehydrogenase and L-Glutamate-Gamma-Semialdehyde Dehydrogenase Molecules V. 29 2024.
ISSN: ESSN 1420-3049
DOI: 10.3390/MOLECULES29225408