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Chlorine in PDB 4qgf: S.Aureus Tmk in Complex with the Potent Inhibitor Compound 38, 2-(3- Chlorophenoxy)-3-Methoxy-4-{(1R)-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Propyl}Benzoic Acid

Enzymatic activity of S.Aureus Tmk in Complex with the Potent Inhibitor Compound 38, 2-(3- Chlorophenoxy)-3-Methoxy-4-{(1R)-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Propyl}Benzoic Acid

All present enzymatic activity of S.Aureus Tmk in Complex with the Potent Inhibitor Compound 38, 2-(3- Chlorophenoxy)-3-Methoxy-4-{(1R)-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Propyl}Benzoic Acid:
2.7.4.9;

Protein crystallography data

The structure of S.Aureus Tmk in Complex with the Potent Inhibitor Compound 38, 2-(3- Chlorophenoxy)-3-Methoxy-4-{(1R)-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Propyl}Benzoic Acid, PDB code: 4qgf 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) 32.94 / 1.83
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.188, 90.557, 48.448, 90.00, 101.92, 90.00
R / Rfree (%) 16.7 / 20.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the S.Aureus Tmk in Complex with the Potent Inhibitor Compound 38, 2-(3- Chlorophenoxy)-3-Methoxy-4-{(1R)-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Propyl}Benzoic Acid (pdb code 4qgf). 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 the Potent Inhibitor Compound 38, 2-(3- Chlorophenoxy)-3-Methoxy-4-{(1R)-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Propyl}Benzoic Acid, PDB code: 4qgf:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4qgf

Go back to Chlorine Binding Sites List in 4qgf
Chlorine binding site 1 out of 2 in the S.Aureus Tmk in Complex with the Potent Inhibitor Compound 38, 2-(3- Chlorophenoxy)-3-Methoxy-4-{(1R)-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Propyl}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 the Potent Inhibitor Compound 38, 2-(3- Chlorophenoxy)-3-Methoxy-4-{(1R)-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Propyl}Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:20.5
occ:1.00
 CL A:32B301 0.0 20.5 1.0
C17 A:32B301 1.7 18.5 1.0
C18 A:32B301 2.7 17.7 1.0
C16 A:32B301 2.7 13.8 1.0
CB A:SER69 3.6 13.5 1.0
CA A:ARG48 3.7 17.7 1.0
OG A:SER69 3.8 14.4 1.0
C13 A:32B301 4.0 17.4 1.0
C15 A:32B301 4.0 15.9 1.0
N A:ARG48 4.0 18.4 1.0
CD1 A:PHE66 4.0 13.7 1.0
CB A:ARG48 4.1 16.9 1.0
CG2 A:ILE47 4.2 18.4 1.0
CG2 A:VAL51 4.2 22.8 1.0
O A:HOH405 4.3 13.1 1.0
CE1 A:PHE66 4.4 13.9 1.0
CA A:PHE66 4.4 9.7 1.0
O A:LEU65 4.4 12.3 1.0
C14 A:32B301 4.5 17.9 1.0
C A:ILE47 4.6 21.2 1.0
CB A:VAL51 4.7 24.3 1.0
N A:PHE66 4.8 10.5 1.0
CG A:ARG48 4.8 23.9 1.0
O A:ILE47 4.8 21.4 1.0
C A:LEU65 4.8 13.6 1.0
CG A:PHE66 4.8 12.6 1.0
O A:GLY44 5.0 15.2 1.0
CB A:ILE47 5.0 17.7 1.0

Chlorine binding site 2 out of 2 in 4qgf

Go back to Chlorine Binding Sites List in 4qgf
Chlorine binding site 2 out of 2 in the S.Aureus Tmk in Complex with the Potent Inhibitor Compound 38, 2-(3- Chlorophenoxy)-3-Methoxy-4-{(1R)-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Propyl}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 the Potent Inhibitor Compound 38, 2-(3- Chlorophenoxy)-3-Methoxy-4-{(1R)-1-[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Propyl}Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:19.3
occ:1.00
 CL B:32B301 0.0 19.3 1.0
C17 B:32B301 1.7 19.6 1.0
C18 B:32B301 2.7 19.3 1.0
C16 B:32B301 2.7 16.7 1.0
CB B:SER69 3.6 14.2 1.0
OG B:SER69 3.7 21.5 1.0
CA B:ARG48 3.8 15.2 1.0
C13 B:32B301 4.0 19.9 1.0
CD1 B:PHE66 4.0 14.1 1.0
C15 B:32B301 4.0 15.2 1.0
N B:ARG48 4.0 15.5 1.0
CB B:ARG48 4.2 15.9 1.0
CG2 B:ILE47 4.2 16.1 1.0
CE1 B:PHE66 4.3 13.9 1.0
CG2 B:VAL51 4.3 17.8 1.0
O B:HOH408 4.3 13.2 1.0
O B:LEU65 4.4 15.3 1.0
CA B:PHE66 4.4 10.3 1.0
C B:ILE47 4.5 17.4 1.0
C14 B:32B301 4.5 17.0 1.0
O B:ILE47 4.6 17.1 1.0
CG B:ARG48 4.7 22.5 1.0
CG B:PHE66 4.7 11.2 1.0
CB B:VAL51 4.7 18.8 1.0
O B:GLY44 4.8 16.9 1.0
N B:PHE66 4.8 10.9 1.0
C B:LEU65 4.8 14.4 1.0
CB B:ILE47 5.0 15.4 1.0
O12 B:32B301 5.0 20.1 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: Fri Jul 26 00:27:53 2024

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