Fluorine in PDB 8dhf: Dhodh in Complex with Ligand 11

All present enzymatic activity of Dhodh in Complex with Ligand 11:
1.3.5.2;

The structure of Dhodh in Complex with Ligand 11, PDB code: 8dhf 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)	78.68 / 1.78
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.85, 90.85, 123.667, 90, 90, 120
R / Rfree (%)	16.2 / 18.1

The structure of Dhodh in Complex with Ligand 11 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Dhodh in Complex with Ligand 11 (pdb code 8dhf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Dhodh in Complex with Ligand 11, PDB code: 8dhf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in the Dhodh in Complex with Ligand 11


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 11 within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:31.7 occ:1.00 F19 A:T6L403 0.0 31.7 1.0 C18 A:T6L403 1.4 28.1 1.0 F21 A:T6L403 2.3 29.9 1.0 F20 A:T6L403 2.3 31.0 1.0 C15 A:T6L403 2.3 25.8 1.0 C17 A:T6L403 2.9 25.5 1.0 CD1 A:LEU50 3.2 36.6 1.0 O14 A:T6L403 3.5 24.4 1.0 CB A:LEU58 3.7 31.2 1.0 CD1 A:LEU58 3.8 39.6 1.0 O A:ALA55 3.9 26.3 1.0 CA A:ALA55 4.0 25.8 1.0 C A:ALA55 4.4 25.2 1.0 CB A:ALA55 4.4 25.6 1.0 CE2 A:PHE62 4.5 42.4 1.0 CG A:LEU58 4.5 36.4 1.0 CD1 A:LEU46 4.5 43.5 1.0 C13 A:T6L403 4.7 24.4 1.0 CB A:LEU46 4.7 39.3 1.0 N A:ALA59 4.7 25.3 1.0 CG A:LEU50 4.7 36.7 1.0 CA A:LEU58 4.9 28.8 1.0 C A:LEU58 4.9 26.7 1.0 N12 A:T6L403 5.0 22.5 1.0

Fluorine binding site 2 out of 5 in the Dhodh in Complex with Ligand 11


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 11 within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:31.0 occ:1.00 F20 A:T6L403 0.0 31.0 1.0 C18 A:T6L403 1.4 28.1 1.0 F21 A:T6L403 2.3 29.9 1.0 F19 A:T6L403 2.3 31.7 1.0 C15 A:T6L403 2.4 25.8 1.0 O14 A:T6L403 2.7 24.4 1.0 N A:ALA59 3.0 25.3 1.0 CA A:ALA59 3.3 25.9 1.0 O A:ALA55 3.4 26.3 1.0 C A:LEU58 3.5 26.7 1.0 C13 A:T6L403 3.6 24.4 1.0 N28 A:T6L403 3.6 27.6 1.0 CB A:ALA59 3.6 26.1 1.0 CB A:LEU58 3.6 31.2 1.0 CD2 A:PHE62 3.7 38.7 1.0 C17 A:T6L403 3.8 25.5 1.0 CE2 A:PHE62 3.8 42.4 1.0 O A:LEU58 4.0 27.9 1.0 CA A:LEU58 4.1 28.8 1.0 N12 A:T6L403 4.2 22.5 1.0 C29 A:T6L403 4.3 31.9 1.0 C22 A:T6L403 4.3 22.9 1.0 C26 A:T6L403 4.4 24.4 1.0 C A:ALA55 4.4 25.2 1.0 F31 A:T6L403 4.8 33.6 1.0 C A:ALA59 4.8 26.6 1.0 C30 A:T6L403 4.8 34.3 1.0 CA A:ALA55 4.8 25.8 1.0 CG A:PHE62 4.8 36.0 1.0 N A:LEU58 4.9 28.0 1.0 CG A:LEU58 4.9 36.4 1.0 CZ A:PHE62 4.9 43.7 1.0 CD1 A:LEU58 5.0 39.6 1.0 C35 A:T6L403 5.0 38.2 1.0

Fluorine binding site 3 out of 5 in the Dhodh in Complex with Ligand 11


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 11 within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:29.9 occ:1.00 F21 A:T6L403 0.0 29.9 1.0 C18 A:T6L403 1.4 28.1 1.0 F20 A:T6L403 2.3 31.0 1.0 F19 A:T6L403 2.3 31.7 1.0 C15 A:T6L403 2.4 25.8 1.0 O14 A:T6L403 2.7 24.4 1.0 C17 A:T6L403 3.0 25.5 1.0 CD1 A:LEU46 3.2 43.5 1.0 N28 A:T6L403 3.6 27.6 1.0 CL36 A:T6L403 3.7 39.7 1.0 CE2 A:PHE62 4.0 42.4 1.0 C13 A:T6L403 4.0 24.4 1.0 C29 A:T6L403 4.1 31.9 1.0 C35 A:T6L403 4.2 38.2 1.0 CD2 A:PHE62 4.3 38.7 1.0 CG A:LEU46 4.4 43.0 1.0 CB A:LEU46 4.5 39.3 1.0 C26 A:T6L403 4.7 24.4 1.0 C22 A:T6L403 4.8 22.9 1.0 N12 A:T6L403 4.9 22.5 1.0 CD2 A:LEU46 5.0 47.0 1.0

Fluorine binding site 4 out of 5 in the Dhodh in Complex with Ligand 11


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Dhodh in Complex with Ligand 11 within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:25.5 occ:1.00 F25 A:T6L403 0.0 25.5 1.0 C24 A:T6L403 1.3 20.8 1.0 C23 A:T6L403 2.3 21.8 1.0 C11 A:T6L403 2.4 21.1 1.0 O5 A:T6L403 2.8 22.4 1.0 N6 A:T6L403 2.9 22.4 1.0 C4 A:T6L403 3.0 25.0 1.0 CG2 A:THR360 3.4 26.6 1.0 CE1 A:TYR356 3.5 20.8 1.0 N12 A:T6L403 3.6 22.5 1.0 C22 A:T6L403 3.6 22.9 1.0 CB A:LEU359 3.7 25.4 0.5 CE1 A:PHE98 3.7 26.7 1.0 CD2 A:LEU359 3.8 22.9 0.5 N A:THR360 3.8 24.8 1.0 CD1 A:PHE98 3.9 23.4 1.0 CB A:LEU359 3.9 23.6 0.5 C A:LEU359 4.0 24.9 1.0 CA A:THR360 4.0 25.7 1.0 CG A:LEU359 4.1 23.4 0.5 N7 A:T6L403 4.1 21.8 1.0 CD1 A:TYR356 4.1 18.9 1.0 C13 A:T6L403 4.1 24.4 1.0 N3 A:T6L403 4.2 22.0 1.0 CB A:THR360 4.3 25.6 1.0 O A:LEU359 4.4 27.5 1.0 CD1 A:LEU359 4.4 25.0 0.5 CA A:LEU359 4.6 24.3 0.5 CZ A:TYR356 4.6 21.0 1.0 CA A:LEU359 4.6 23.7 0.5 OH A:TYR356 4.6 21.4 1.0 C8 A:T6L403 4.7 22.9 1.0 CG A:LEU359 4.8 24.7 0.5 O A:TYR356 4.8 18.7 1.0 CB A:ALA59 4.8 26.1 1.0 C26 A:T6L403 4.8 24.4 1.0 CZ A:PHE98 4.9 26.6 1.0 O27 A:T6L403 5.0 28.7 1.0

Fluorine binding site 5 out of 5 in the Dhodh in Complex with Ligand 11


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Dhodh in Complex with Ligand 11 within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:33.6 occ:1.00 F31 A:T6L403 0.0 33.6 1.0 C30 A:T6L403 1.4 34.3 1.0 C32 A:T6L403 2.4 36.3 1.0 C29 A:T6L403 2.4 31.9 1.0 N28 A:T6L403 2.7 27.6 1.0 OG1 A:THR63 3.0 26.4 1.0 O27 A:T6L403 3.1 28.7 1.0 C26 A:T6L403 3.1 24.4 1.0 O A:ALA59 3.3 25.8 1.0 C35 A:T6L403 3.6 38.2 1.0 C33 A:T6L403 3.7 33.0 1.0 CA A:ALA59 3.7 25.9 1.0 C A:ALA59 3.9 26.6 1.0 CB A:ALA59 3.9 26.1 1.0 CB A:PHE62 4.0 33.3 1.0 C34 A:T6L403 4.2 38.5 1.0 C22 A:T6L403 4.2 22.9 1.0 N A:THR63 4.2 28.6 1.0 CB A:THR63 4.3 27.4 1.0 CE A:MET111 4.5 35.2 1.0 CD2 A:LEU68 4.5 50.9 1.0 CG A:PRO364 4.5 29.0 1.0 CA A:THR63 4.6 28.5 1.0 CD2 A:PHE62 4.6 38.7 1.0 F20 A:T6L403 4.8 31.0 1.0 C A:PHE62 4.8 30.3 1.0 C23 A:T6L403 4.8 21.8 1.0 CG A:PHE62 4.9 36.0 1.0 CA A:PHE62 4.9 31.8 1.0 N A:ALA59 5.0 25.3 1.0 C13 A:T6L403 5.0 24.4 1.0

J.S.Cisar, C.Pietsch, L.G.Deratt, E.Jacoby, F.Kazmi, C.Keohane, K.Legenski, R.Matico, P.Shaffer, Y.Simonnet, A.Tanner, C.Y.Wang, W.Wang, R.Attar, J.P.Edwards, S.D.Kuduk. N -Heterocyclic 3-Pyridyl Carboxamide Inhibitors of Dhodh For the Treatment of Acute Myelogenous Leukemia. J.Med.Chem. V. 65 11241 2022.
ISSN: ISSN 0022-2623
PubMed: 35925768
DOI: 10.1021/ACS.JMEDCHEM.2C00788