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Fluorine in PDB 4qga: S.Aureus Tmk in Complex with Potent Inhibitor Compound 19, 2-(3- Chlorophenoxy)-3-Fluoro-4-{[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Methyl}Benzoic Acid

Enzymatic activity of S.Aureus Tmk in Complex with Potent Inhibitor Compound 19, 2-(3- Chlorophenoxy)-3-Fluoro-4-{[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Methyl}Benzoic Acid

All present enzymatic activity of S.Aureus Tmk in Complex with Potent Inhibitor Compound 19, 2-(3- Chlorophenoxy)-3-Fluoro-4-{[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Methyl}Benzoic Acid:
2.7.4.9;

Protein crystallography data

The structure of S.Aureus Tmk in Complex with Potent Inhibitor Compound 19, 2-(3- Chlorophenoxy)-3-Fluoro-4-{[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Methyl}Benzoic Acid, PDB code: 4qga 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) 21.05 / 1.94
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.780, 90.841, 48.221, 90.00, 102.88, 90.00
R / Rfree (%) 19.2 / 21.7

Other elements in 4qga:

The structure of S.Aureus Tmk in Complex with Potent Inhibitor Compound 19, 2-(3- Chlorophenoxy)-3-Fluoro-4-{[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Methyl}Benzoic Acid also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the S.Aureus Tmk in Complex with Potent Inhibitor Compound 19, 2-(3- Chlorophenoxy)-3-Fluoro-4-{[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Methyl}Benzoic Acid (pdb code 4qga). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the S.Aureus Tmk in Complex with Potent Inhibitor Compound 19, 2-(3- Chlorophenoxy)-3-Fluoro-4-{[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Methyl}Benzoic Acid, PDB code: 4qga:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4qga

Go back to Fluorine Binding Sites List in 4qga
Fluorine binding site 1 out of 2 in the S.Aureus Tmk in Complex with Potent Inhibitor Compound 19, 2-(3- Chlorophenoxy)-3-Fluoro-4-{[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Methyl}Benzoic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of S.Aureus Tmk in Complex with Potent Inhibitor Compound 19, 2-(3- Chlorophenoxy)-3-Fluoro-4-{[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Methyl}Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:30.2
occ:1.00
 F23 A:31Z301 0.0 30.2 1.0
C22 A:31Z301 1.4 31.2 1.0
C21 A:31Z301 2.3 30.3 1.0
C17 A:31Z301 2.4 31.2 1.0
O24 A:31Z301 2.7 30.2 1.0
C16 A:31Z301 2.9 29.4 1.0
C15 A:31Z301 3.1 29.6 1.0
C25 A:31Z301 3.2 31.2 1.0
CZ A:PHE66 3.4 28.0 1.0
N14 A:31Z301 3.6 29.7 1.0
C20 A:31Z301 3.6 32.4 1.0
C18 A:31Z301 3.6 30.6 1.0
CE1 A:PHE66 3.6 30.0 1.0
C26 A:31Z301 3.7 32.0 1.0
C30 A:31Z301 3.9 32.2 1.0
C19 A:31Z301 4.1 30.1 1.0
CG1 A:VAL51 4.2 30.1 1.0
C10 A:31Z301 4.4 29.2 1.0
CD2 A:LEU52 4.6 41.5 1.0
CE2 A:PHE66 4.6 29.6 1.0
C27 A:31Z301 4.7 28.0 1.0
N4 A:31Z301 4.7 30.0 1.0
C13 A:31Z301 4.7 29.1 1.0
C32 A:31Z301 4.9 37.3 1.0
C29 A:31Z301 4.9 30.8 1.0

Fluorine binding site 2 out of 2 in 4qga

Go back to Fluorine Binding Sites List in 4qga
Fluorine binding site 2 out of 2 in the S.Aureus Tmk in Complex with Potent Inhibitor Compound 19, 2-(3- Chlorophenoxy)-3-Fluoro-4-{[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Methyl}Benzoic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of S.Aureus Tmk in Complex with Potent Inhibitor Compound 19, 2-(3- Chlorophenoxy)-3-Fluoro-4-{[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Methyl}Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:29.9
occ:1.00
 F23 B:31Z301 0.0 29.9 1.0
C22 B:31Z301 1.3 29.7 1.0
C21 B:31Z301 2.3 31.1 1.0
C17 B:31Z301 2.4 30.4 1.0
O24 B:31Z301 2.7 31.8 1.0
C16 B:31Z301 2.9 28.6 1.0
C25 B:31Z301 3.2 28.6 1.0
C15 B:31Z301 3.2 26.7 1.0
CZ B:PHE66 3.4 26.0 1.0
C20 B:31Z301 3.6 32.2 1.0
N14 B:31Z301 3.6 27.6 1.0
C18 B:31Z301 3.6 30.9 1.0
C26 B:31Z301 3.7 26.4 1.0
CE1 B:PHE66 3.8 27.4 1.0
C30 B:31Z301 3.9 26.4 1.0
C19 B:31Z301 4.1 31.6 1.0
CG1 B:VAL51 4.3 31.3 1.0
CD2 B:LEU52 4.5 38.9 1.0
CE2 B:PHE66 4.5 26.9 1.0
C10 B:31Z301 4.6 26.1 1.0
C27 B:31Z301 4.7 25.8 1.0
C13 B:31Z301 4.8 26.8 1.0
C32 B:31Z301 4.8 33.9 1.0
N4 B:31Z301 4.9 25.0 1.0
C29 B:31Z301 4.9 27.1 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: Sun Dec 13 12:11:25 2020

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