Fluorine in PDB 7k2u: Dhodh in Complex with Ligand 13

All present enzymatic activity of Dhodh in Complex with Ligand 13:
1.3.5.2;

The structure of Dhodh in Complex with Ligand 13, PDB code: 7k2u was solved by P.L.Shaffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	78.47 / 1.73
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.607, 90.607, 122.749, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 17.9

The binding sites of Fluorine atom in the Dhodh in Complex with Ligand 13 (pdb code 7k2u). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Dhodh in Complex with Ligand 13, PDB code: 7k2u:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Dhodh in Complex with Ligand 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dhodh in Complex with Ligand 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:25.5 occ:1.00 F15 A:VU7403 0.0 25.5 1.0 C14 A:VU7403 1.3 22.0 1.0 C16 A:VU7403 2.3 20.0 1.0 C13 A:VU7403 2.4 19.2 1.0 CG1 A:VAL134 3.1 18.7 1.0 C12 A:VU7403 3.6 19.4 1.0 C17 A:VU7403 3.6 19.0 1.0 C7M A:FMN401 3.7 15.1 1.0 CG1 A:VAL143 4.0 17.5 1.0 C11 A:VU7403 4.1 20.0 1.0 CB A:VAL134 4.4 18.1 1.0 CB A:PRO52 4.5 23.5 1.0 O A:PRO52 4.6 20.1 1.0 OH A:TYR356 4.7 16.4 1.0 CG2 A:VAL134 4.7 20.6 1.0 CG2 A:THR360 4.8 18.4 1.0 CG2 A:VAL143 4.8 16.3 1.0 CB A:HIS56 4.8 18.2 1.0 ND1 A:HIS56 4.9 17.9 1.0 C6 A:VU7403 4.9 20.1 1.0 C A:PRO52 4.9 20.9 1.0 CB A:VAL143 5.0 15.4 1.0

Fluorine binding site 2 out of 3 in the Dhodh in Complex with Ligand 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dhodh in Complex with Ligand 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:24.6 occ:0.30 F30 A:VU7403 0.0 24.6 0.3 C25 A:VU7403 1.3 25.2 0.7 C29 A:VU7403 1.3 23.6 0.3 C26 A:VU7403 2.3 29.6 0.7 C28 A:VU7403 2.4 25.3 0.3 C24 A:VU7403 2.4 22.2 1.0 C21 A:VU7403 2.9 20.2 1.0 C22 A:VU7403 3.2 20.9 1.0 SD A:MET43 3.4 23.2 1.0 CD2 A:LEU42 3.5 33.8 1.0 C27 A:VU7403 3.5 25.9 0.7 C27 A:VU7403 3.6 23.9 0.3 CE2 A:TYR38 3.6 25.7 1.0 C25 A:VU7403 3.6 22.9 0.3 C29 A:VU7403 3.6 24.2 0.7 O4 A:PGE412 3.8 68.7 1.0 CD1 A:LEU46 3.8 36.7 1.0 C20 A:VU7403 4.0 19.1 1.0 CD A:PRO364 4.1 21.3 1.0 C28 A:VU7403 4.1 24.5 0.7 C26 A:VU7403 4.1 23.0 0.3 CD2 A:TYR38 4.1 24.9 1.0 C23 A:VU7403 4.3 20.6 1.0 CE A:MET43 4.4 22.7 1.0 O3 A:PGE412 4.4 65.1 1.0 CG A:PRO364 4.8 23.0 1.0 CZ A:TYR38 4.8 28.7 1.0 C6 A:PGE412 4.8 65.8 1.0 F30 A:VU7403 4.8 26.1 0.7 C5 A:PGE412 4.8 62.0 1.0 CG A:LEU42 4.9 32.6 1.0 CG A:MET43 5.0 22.3 1.0 C19 A:VU7403 5.0 18.6 1.0 OH A:TYR38 5.0 31.1 1.0

Fluorine binding site 3 out of 3 in the Dhodh in Complex with Ligand 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dhodh in Complex with Ligand 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:26.1 occ:0.70 F30 A:VU7403 0.0 26.1 0.7 C25 A:VU7403 1.3 22.9 0.3 C29 A:VU7403 1.4 24.2 0.7 C26 A:VU7403 2.3 23.0 0.3 C28 A:VU7403 2.4 24.5 0.7 C24 A:VU7403 2.4 22.2 1.0 C21 A:VU7403 2.8 20.2 1.0 OG1 A:THR63 3.0 21.4 1.0 C20 A:VU7403 3.0 19.1 1.0 O A:ALA59 3.3 21.2 1.0 CB A:ALA59 3.4 19.4 1.0 CA A:ALA59 3.5 20.3 1.0 C27 A:VU7403 3.6 23.9 0.3 C27 A:VU7403 3.6 25.9 0.7 C29 A:VU7403 3.7 23.6 0.3 C25 A:VU7403 3.7 25.2 0.7 C A:ALA59 3.8 21.7 1.0 C22 A:VU7403 3.9 20.9 1.0 C19 A:VU7403 4.1 18.6 1.0 C28 A:VU7403 4.1 25.3 0.3 C26 A:VU7403 4.2 29.6 0.7 CE A:MET111 4.2 23.9 1.0 CB A:THR63 4.4 22.8 1.0 CZ A:PHE98 4.4 22.6 1.0 CG A:PRO364 4.4 23.0 1.0 N A:THR63 4.7 23.5 1.0 C23 A:VU7403 4.8 20.6 1.0 F30 A:VU7403 4.8 24.6 0.3 CD A:PRO364 4.8 21.3 1.0 C18 A:VU7403 4.9 20.5 1.0 N A:ALA59 4.9 20.6 1.0 CD2 A:LEU68 4.9 30.7 1.0 CB A:PHE62 5.0 26.7 1.0 N A:VAL60 5.0 20.9 1.0 CA A:THR63 5.0 23.6 1.0

L.G.Deratt, E.Christine Pietsch, A.Tanner, P.Shaffer, E.Jacoby, W.Wang, F.Kazmi, X.Zhang, R.M.Attar, J.P.Edwards, S.D.Kuduk. A Carboxylic Acid Isostere Screen of the Dhodh Inhibitor Brequinar. Bioorg.Med.Chem.Lett. V. 30 27589 2020.
ISSN: ESSN 1464-3405
PubMed: 33007394
DOI: 10.1016/J.BMCL.2020.127589