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

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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy