Atomistry » Chlorine » PDB 4q69-4qgp » 4qgf
Atomistry »
  Chlorine »
    PDB 4q69-4qgp »
      4qgf »

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 11 20:47:00 2025

Last articles

Fe in 7R2S
Fe in 7R0W
Fe in 7R2R
Fe in 7R2P
Fe in 7R2O
Fe in 7R1J
Fe in 7R1I
Fe in 7QWT
Fe in 7R1H
Fe in 7R0F
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy