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Chlorine 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:

Fluorine (F) 2 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 2 in 4qgg

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

b:28.2
occ:1.00
 CL A:32C301 0.0 28.2 1.0
C33 A:32C301 1.7 29.6 1.0
C34 A:32C301 2.7 29.4 1.0
C32 A:32C301 2.7 25.5 1.0
CB A:SER69 3.6 21.0 1.0
OG A:SER69 3.7 27.0 1.0
CA A:ARG48 3.8 26.9 1.0
CG2 A:VAL51 3.9 37.4 1.0
C29 A:32C301 4.0 30.3 1.0
CD1 A:PHE66 4.0 24.7 1.0
N A:ARG48 4.0 26.9 1.0
C31 A:32C301 4.0 27.4 1.0
CG2 A:ILE47 4.1 26.9 1.0
CB A:ARG48 4.1 25.2 1.0
O A:LEU65 4.2 22.4 1.0
CE1 A:PHE66 4.3 25.4 1.0
CA A:PHE66 4.4 21.1 1.0
C A:ILE47 4.4 29.5 1.0
O A:HOH410 4.4 21.8 1.0
C30 A:32C301 4.5 29.1 1.0
CB A:VAL51 4.5 37.5 1.0
O A:ILE47 4.6 28.5 1.0
C A:LEU65 4.7 21.9 1.0
N A:PHE66 4.7 21.0 1.0
CG A:PHE66 4.8 23.1 1.0
CB A:ILE47 4.9 26.2 1.0
CG A:ARG48 4.9 26.4 1.0
O A:GLY44 4.9 30.1 1.0
CG1 A:VAL51 5.0 36.7 1.0

Chlorine binding site 2 out of 2 in 4qgg

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

b:30.3
occ:1.00
 CL B:32C301 0.0 30.3 1.0
C33 B:32C301 1.7 25.6 1.0
C34 B:32C301 2.7 25.2 1.0
C32 B:32C301 2.7 23.7 1.0
CB B:SER69 3.5 23.3 1.0
OG B:SER69 3.5 28.0 1.0
CA B:ARG48 3.8 25.4 1.0
CG2 B:VAL51 3.9 32.4 1.0
CD1 B:PHE66 4.0 25.6 1.0
C29 B:32C301 4.0 24.1 1.0
CG2 B:ILE47 4.0 27.3 1.0
C31 B:32C301 4.0 24.1 1.0
N B:ARG48 4.0 26.4 1.0
CB B:ARG48 4.1 23.1 1.0
CE1 B:PHE66 4.2 25.3 1.0
O B:LEU65 4.3 21.5 1.0
O B:HOH463 4.4 27.1 1.0
C B:ILE47 4.4 28.4 1.0
CA B:PHE66 4.5 19.3 1.0
C30 B:32C301 4.5 26.2 1.0
O B:ILE47 4.5 27.4 1.0
CB B:VAL51 4.6 33.2 1.0
O B:GLY44 4.7 26.3 1.0
C B:LEU65 4.7 22.0 1.0
CG B:PHE66 4.8 21.6 1.0
N B:PHE66 4.8 19.1 1.0
CB B:ILE47 4.8 26.0 1.0
CG B:ARG48 4.8 26.2 1.0
CA B:SER69 5.0 21.8 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 26 00:27:54 2024

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