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Fluorine in PDB 4qgg: Tmk in Complex with Compound 46, 2-(3-Chlorophenoxy)-3-Fluoro-4-{(1R)- 3-Methyl-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Piperidin-1-Yl]Butyl}Benzoic Acid

Enzymatic activity of Tmk in Complex with Compound 46, 2-(3-Chlorophenoxy)-3-Fluoro-4-{(1R)- 3-Methyl-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Piperidin-1-Yl]Butyl}Benzoic Acid

All present enzymatic activity of Tmk in Complex with Compound 46, 2-(3-Chlorophenoxy)-3-Fluoro-4-{(1R)- 3-Methyl-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Piperidin-1-Yl]Butyl}Benzoic Acid:
2.7.4.9;

Protein crystallography data

The structure of Tmk in Complex with Compound 46, 2-(3-Chlorophenoxy)-3-Fluoro-4-{(1R)- 3-Methyl-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Piperidin-1-Yl]Butyl}Benzoic Acid, PDB code: 4qgg was solved by N.B.Olivier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.67 / 1.62
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.996, 91.042, 48.504, 90.00, 100.63, 90.00
R / Rfree (%) 20.8 / 22.2

Other elements in 4qgg:

The structure of Tmk in Complex with Compound 46, 2-(3-Chlorophenoxy)-3-Fluoro-4-{(1R)- 3-Methyl-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Piperidin-1-Yl]Butyl}Benzoic Acid also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Tmk in Complex with Compound 46, 2-(3-Chlorophenoxy)-3-Fluoro-4-{(1R)- 3-Methyl-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Piperidin-1-Yl]Butyl}Benzoic Acid (pdb code 4qgg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Tmk in Complex with Compound 46, 2-(3-Chlorophenoxy)-3-Fluoro-4-{(1R)- 3-Methyl-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Piperidin-1-Yl]Butyl}Benzoic Acid, PDB code: 4qgg:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4qgg

Go back to Fluorine Binding Sites List in 4qgg
Fluorine binding site 1 out of 2 in the Tmk in Complex with Compound 46, 2-(3-Chlorophenoxy)-3-Fluoro-4-{(1R)- 3-Methyl-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Piperidin-1-Yl]Butyl}Benzoic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Tmk in Complex with Compound 46, 2-(3-Chlorophenoxy)-3-Fluoro-4-{(1R)- 3-Methyl-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Piperidin-1-Yl]Butyl}Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:33.6
occ:1.00
 F27 A:32C301 0.0 33.6 1.0
C26 A:32C301 1.3 33.0 1.0
C25 A:32C301 2.3 29.8 1.0
C21 A:32C301 2.4 31.1 1.0
O28 A:32C301 2.7 28.6 1.0
C29 A:32C301 3.0 30.3 1.0
C17 A:32C301 3.0 31.0 1.0
C16 A:32C301 3.0 29.6 1.0
C18 A:32C301 3.2 34.7 1.0
C15 A:32C301 3.3 22.0 1.0
CZ A:PHE66 3.4 25.0 1.0
C30 A:32C301 3.5 29.1 1.0
CE1 A:PHE66 3.5 25.4 1.0
C34 A:32C301 3.6 29.4 1.0
C24 A:32C301 3.6 29.5 1.0
C22 A:32C301 3.6 29.9 1.0
N14 A:32C301 3.7 28.2 1.0
C20 A:32C301 3.9 35.1 1.0
CG1 A:VAL51 4.0 36.7 1.0
C23 A:32C301 4.1 28.9 1.0
CD2 A:LEU52 4.2 37.7 1.0
C31 A:32C301 4.4 27.4 1.0
C33 A:32C301 4.5 29.6 1.0
C19 A:32C301 4.5 37.4 1.0
CE2 A:PHE66 4.7 26.3 1.0
C10 A:32C301 4.7 21.3 1.0
C13 A:32C301 4.8 24.4 1.0
C36 A:32C301 4.8 32.7 1.0
C32 A:32C301 4.8 25.5 1.0
CD1 A:PHE66 4.8 24.7 1.0
O A:HOH430 5.0 31.9 1.0

Fluorine binding site 2 out of 2 in 4qgg

Go back to Fluorine Binding Sites List in 4qgg
Fluorine binding site 2 out of 2 in the Tmk in Complex with Compound 46, 2-(3-Chlorophenoxy)-3-Fluoro-4-{(1R)- 3-Methyl-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Piperidin-1-Yl]Butyl}Benzoic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Tmk in Complex with Compound 46, 2-(3-Chlorophenoxy)-3-Fluoro-4-{(1R)- 3-Methyl-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Piperidin-1-Yl]Butyl}Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:29.6
occ:1.00
 F27 B:32C301 0.0 29.6 1.0
C26 B:32C301 1.3 29.7 1.0
C25 B:32C301 2.3 29.6 1.0
C21 B:32C301 2.4 31.0 1.0
O28 B:32C301 2.7 28.1 1.0
C17 B:32C301 2.9 31.3 1.0
C16 B:32C301 3.0 29.5 1.0
C29 B:32C301 3.0 24.1 1.0
C15 B:32C301 3.2 26.3 1.0
C18 B:32C301 3.3 32.9 1.0
CZ B:PHE66 3.4 25.6 1.0
C30 B:32C301 3.6 26.2 1.0
C22 B:32C301 3.6 32.5 1.0
C24 B:32C301 3.6 32.1 1.0
N14 B:32C301 3.6 29.4 1.0
CE1 B:PHE66 3.6 25.3 1.0
C34 B:32C301 3.7 25.2 1.0
C19 B:32C301 4.0 32.4 1.0
CG1 B:VAL51 4.0 32.9 1.0
C23 B:32C301 4.1 31.7 1.0
CD2 B:LEU52 4.4 38.6 1.0
C31 B:32C301 4.5 24.1 1.0
C10 B:32C301 4.6 23.6 1.0
C33 B:32C301 4.6 25.6 1.0
CE2 B:PHE66 4.6 26.1 1.0
C20 B:32C301 4.7 35.6 1.0
C13 B:32C301 4.7 28.8 1.0
C36 B:32C301 4.8 31.9 1.0
N4 B:32C301 4.9 23.1 1.0
O B:HOH417 5.0 29.7 1.0
C32 B:32C301 5.0 23.7 1.0
CD1 B:PHE66 5.0 25.6 1.0

Reference:

S.P.Kawatkar, T.A.Keating, N.B.Olivier, J.N.Breen, O.M.Green, S.Y.Guler, M.F.Hentemann, J.T.Loch, A.R.Mckenzie, J.V.Newman, L.G.Otterson, G.Martinez-Botella. Antibacterial Inhibitors of Gram-Positive Thymidylate Kinase: Structure-Activity Relationships and Chiral Preference of A New Hydrophobic Binding Region. J.Med.Chem. V. 57 4584 2014.
ISSN: ISSN 0022-2623
PubMed: 24828090
DOI: 10.1021/JM500463C
Page generated: Thu Aug 1 05:11:46 2024

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