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Chlorine in PDB 4qg7: S.Aureus Tmk in Complex with A Potent Inhibitor Compound 18, 2-(3- Chlorophenoxy)-3-Methoxy-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 A Potent Inhibitor Compound 18, 2-(3- Chlorophenoxy)-3-Methoxy-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 A Potent Inhibitor Compound 18, 2-(3- Chlorophenoxy)-3-Methoxy-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 A Potent Inhibitor Compound 18, 2-(3- Chlorophenoxy)-3-Methoxy-4-{[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Methyl}Benzoic Acid, PDB code: 4qg7 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) 45.22 / 1.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.040, 90.450, 48.370, 90.00, 102.10, 90.00
R / Rfree (%) 18.7 / 21.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the S.Aureus Tmk in Complex with A Potent Inhibitor Compound 18, 2-(3- Chlorophenoxy)-3-Methoxy-4-{[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Methyl}Benzoic Acid (pdb code 4qg7). 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 A Potent Inhibitor Compound 18, 2-(3- Chlorophenoxy)-3-Methoxy-4-{[(3S)-3-(5-Methyl-2,4-Dioxo-3,4- Dihydropyrimidin-1(2H)-Yl)Piperidin-1-Yl]Methyl}Benzoic Acid, PDB code: 4qg7:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4qg7

Go back to Chlorine Binding Sites List in 4qg7
Chlorine binding site 1 out of 2 in the S.Aureus Tmk in Complex with A Potent Inhibitor Compound 18, 2-(3- Chlorophenoxy)-3-Methoxy-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 A Potent Inhibitor Compound 18, 2-(3- Chlorophenoxy)-3-Methoxy-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:21.7
occ:1.00
 CL A:32K301 0.0 21.7 1.0
C30 A:32K301 1.7 20.6 1.0
C31 A:32K301 2.7 19.8 1.0
C29 A:32K301 2.7 18.2 1.0
CB A:SER69 3.7 16.1 1.0
CA A:ARG48 3.8 20.4 1.0
OG A:SER69 3.9 15.5 1.0
C26 A:32K301 3.9 19.9 1.0
C28 A:32K301 4.0 18.2 1.0
CD1 A:PHE66 4.0 17.2 1.0
CG2 A:VAL51 4.1 30.1 1.0
N A:ARG48 4.1 19.5 1.0
CB A:ARG48 4.1 19.8 1.0
CG2 A:ILE47 4.2 19.6 1.0
CE1 A:PHE66 4.3 17.5 1.0
O A:LEU65 4.4 15.3 1.0
O A:HOH406 4.4 14.8 1.0
CA A:PHE66 4.4 13.5 1.0
C27 A:32K301 4.5 19.9 1.0
C A:ILE47 4.5 22.7 1.0
CB A:VAL51 4.5 31.1 1.0
O A:ILE47 4.7 23.7 1.0
C A:LEU65 4.7 16.1 1.0
N A:PHE66 4.7 14.9 1.0
CG A:ARG48 4.7 23.4 1.0
CG A:PHE66 4.8 15.8 1.0
CG1 A:VAL51 4.9 30.7 1.0
O25 A:32K301 5.0 18.9 1.0
O A:GLY44 5.0 18.4 1.0

Chlorine binding site 2 out of 2 in 4qg7

Go back to Chlorine Binding Sites List in 4qg7
Chlorine binding site 2 out of 2 in the S.Aureus Tmk in Complex with A Potent Inhibitor Compound 18, 2-(3- Chlorophenoxy)-3-Methoxy-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 A Potent Inhibitor Compound 18, 2-(3- Chlorophenoxy)-3-Methoxy-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:19.9
occ:1.00
 CL B:32K301 0.0 19.9 1.0
C30 B:32K301 1.7 21.0 1.0
C31 B:32K301 2.7 18.7 1.0
C29 B:32K301 2.7 18.5 1.0
CB B:SER69 3.7 17.0 1.0
CA B:ARG48 3.8 18.7 1.0
OG B:SER69 3.9 18.7 1.0
C26 B:32K301 4.0 20.3 1.0
CD1 B:PHE66 4.0 17.6 1.0
C28 B:32K301 4.0 19.2 1.0
N B:ARG48 4.0 19.7 1.0
CG2 B:VAL51 4.1 21.5 1.0
CB B:ARG48 4.1 17.2 1.0
CG2 B:ILE47 4.2 21.6 1.0
CE1 B:PHE66 4.3 17.4 1.0
O B:LEU65 4.3 14.9 1.0
O B:HOH411 4.4 16.2 1.0
CA B:PHE66 4.4 12.9 1.0
C B:ILE47 4.5 21.5 1.0
C27 B:32K301 4.5 18.7 1.0
CB B:VAL51 4.6 21.7 1.0
O B:ILE47 4.6 20.6 1.0
C B:LEU65 4.7 15.6 1.0
N B:PHE66 4.7 13.2 1.0
CG B:PHE66 4.7 14.7 1.0
CG B:ARG48 4.8 21.4 1.0
O B:GLY44 4.9 21.0 1.0
CB B:ILE47 5.0 19.7 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 00:27:14 2024

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