Atomistry » Chlorine » PDB 4q63-4qgo » 4qga
Atomistry »
  Chlorine »
    PDB 4q63-4qgo »
      4qga »

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 26 00:27:19 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy