Atomistry » Fluorine » PDB 4zga-4zzi » 4zt4
Atomistry »
  Fluorine »
    PDB 4zga-4zzi »
      4zt4 »

Fluorine in PDB 4zt4: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708), PDB code: 4zt4 was solved by C.-Y.Koh, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.59 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.516, 106.128, 207.106, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 22.5

Other elements in 4zt4:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708) also contains other interesting chemical elements:

Arsenic (As) 2 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708) (pdb code 4zt4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708), PDB code: 4zt4:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4zt4

Go back to Fluorine Binding Sites List in 4zt4
Fluorine binding site 1 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:63.5
occ:1.00
 F B:4RO803 0.0 63.5 1.0
C B:4RO803 1.4 64.3 1.0
F1 B:4RO803 2.2 61.4 1.0
C9 B:4RO803 2.4 64.4 1.0
C1 B:4RO803 2.5 62.9 1.0
N B:4RO803 2.9 64.4 1.0
N1 B:4RO803 3.7 63.5 1.0
O B:HOH1105 3.9 54.2 1.0
C2 B:4RO803 4.3 62.8 1.0
C10 B:4RO803 4.7 62.0 1.0
CD2 B:TYR250 4.8 55.5 1.0
N2 B:4RO803 4.9 60.1 1.0
CE2 B:TYR250 4.9 56.5 1.0
CG B:TYR250 5.0 54.7 1.0

Fluorine binding site 2 out of 2 in 4zt4

Go back to Fluorine Binding Sites List in 4zt4
Fluorine binding site 2 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:61.4
occ:1.00
 F1 B:4RO803 0.0 61.4 1.0
C B:4RO803 1.4 64.3 1.0
F B:4RO803 2.2 63.5 1.0
C9 B:4RO803 2.4 64.4 1.0
C1 B:4RO803 2.5 62.9 1.0
N1 B:4RO803 3.0 63.5 1.0
N B:4RO803 3.1 64.4 1.0
O B:HOH1105 3.2 54.2 1.0
CG2 B:VAL473 3.5 50.9 1.0
C10 B:4RO803 3.6 62.0 1.0
N2 B:4RO803 3.8 60.1 1.0
CG1 B:VAL473 3.9 53.3 1.0
CB B:VAL473 4.0 51.0 1.0
C2 B:4RO803 4.4 62.8 1.0
C4 B:4RO803 4.4 58.9 1.0
N4 B:4RO803 4.6 61.5 1.0
C3 B:4RO803 4.8 63.0 1.0
C11 B:4RO803 5.0 58.8 1.0

Reference:

Z.Zhang, C.Y.Koh, R.M.Ranade, S.Shibata, J.R.Gillespie, M.A.Hulverson, W.Huang, J.Nguyen, N.Pendem, M.H.Gelb, C.L.Verlinde, W.G.Hol, F.S.Buckner, E.Fan. 5-Fluoroimidazo[4,5-B]Pyridine Is A Privileged Fragment That Conveys Bioavailability to Potent Trypanosomal Methionyl-Trna Synthetase Inhibitors. Acs Infect Dis. V. 2 399 2016.
ISSN: ESSN 2373-8227
PubMed: 27627628
DOI: 10.1021/ACSINFECDIS.6B00036
Page generated: Thu Aug 1 07:26:21 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