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Chlorine 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:

Fluorine (F) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4qga

Go back to Chlorine Binding Sites List in 4qga
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl301

b:32.1
occ:1.00
 CL A:31Z301 0.0 32.1 1.0
C29 A:31Z301 1.7 30.8 1.0
C30 A:31Z301 2.7 32.2 1.0
C28 A:31Z301 2.7 26.5 1.0
CB A:SER69 3.6 25.6 1.0
CA A:ARG48 3.7 28.7 1.0
OG A:SER69 3.7 29.4 1.0
CG2 A:VAL51 3.9 29.5 1.0
N A:ARG48 4.0 27.4 1.0
C25 A:31Z301 4.0 31.2 1.0
C27 A:31Z301 4.0 28.0 1.0
CB A:ARG48 4.0 28.7 1.0
CD1 A:PHE66 4.1 29.1 1.0
CG2 A:ILE47 4.1 26.9 1.0
CE1 A:PHE66 4.4 30.0 1.0
O A:LEU65 4.4 23.4 1.0
C A:ILE47 4.4 29.1 1.0
CB A:VAL51 4.5 30.8 1.0
CA A:PHE66 4.5 23.4 1.0
C26 A:31Z301 4.5 32.0 1.0
O A:HOH406 4.5 23.6 1.0
O A:ILE47 4.6 29.7 1.0
CG A:ARG48 4.7 31.9 1.0
C A:LEU65 4.7 24.9 1.0
N A:PHE66 4.8 24.3 1.0
O A:GLY44 4.8 28.1 1.0
CB A:ILE47 4.9 26.7 1.0
CG A:PHE66 4.9 27.0 1.0
CG1 A:VAL51 5.0 30.1 1.0

Chlorine binding site 2 out of 2 in 4qga

Go back to Chlorine Binding Sites List in 4qga
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl301

b:28.0
occ:1.00
 CL B:31Z301 0.0 28.0 1.0
C29 B:31Z301 1.7 27.1 1.0
C30 B:31Z301 2.7 26.4 1.0
C28 B:31Z301 2.7 24.7 1.0
CB B:SER69 3.6 25.7 1.0
OG B:SER69 3.7 31.9 1.0
CA B:ARG48 3.7 22.5 1.0
N B:ARG48 3.9 22.7 1.0
C25 B:31Z301 4.0 28.6 1.0
CG2 B:VAL51 4.0 30.9 1.0
C27 B:31Z301 4.0 25.8 1.0
CD1 B:PHE66 4.0 26.7 1.0
CG2 B:ILE47 4.1 25.6 1.0
CB B:ARG48 4.2 21.7 1.0
O B:LEU65 4.3 23.6 1.0
CE1 B:PHE66 4.3 27.4 1.0
O B:HOH407 4.3 23.2 1.0
C B:ILE47 4.4 25.0 1.0
C26 B:31Z301 4.5 26.4 1.0
CA B:PHE66 4.5 19.2 1.0
CB B:VAL51 4.5 31.7 1.0
O B:ILE47 4.5 23.6 1.0
O B:GLY44 4.7 25.0 1.0
CG B:ARG48 4.7 32.7 1.0
C B:LEU65 4.7 24.2 1.0
CG B:PHE66 4.7 22.4 1.0
N B:PHE66 4.9 19.4 1.0
CB B:ILE47 4.9 23.9 1.0
C B:ARG48 4.9 27.7 1.0
CG1 B:VAL51 5.0 31.3 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: Fri Jul 11 20:46:56 2025

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