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Fluorine in PDB 4c0c: Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(2,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide.

Enzymatic activity of Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(2,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide.

All present enzymatic activity of Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(2,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide.:
1.14.13.70;

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(2,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide., PDB code: 4c0c was solved by C.M.Calvet, D.F.Vieira, J.Y.Choi, M.D.Cameron, J.Gut, D.Kellar, J.L.Siqueira-Neto, J.H.Mckerrow, W.R.Roush, L.M.Podust, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.68 / 2.04
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 128.528, 128.528, 116.721, 90.00, 90.00, 120.00
R / Rfree (%) 19.927 / 25.365

Other elements in 4c0c:

The structure of Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(2,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide. also contains other interesting chemical elements:

Iron (Fe) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(2,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide. (pdb code 4c0c). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(2,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide., PDB code: 4c0c:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4c0c

Go back to Fluorine Binding Sites List in 4c0c
Fluorine binding site 1 out of 3 in the Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(2,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(2,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1460

b:31.7
occ:1.00
 F2 A:WVH1460 0.0 31.7 1.0
C23 A:WVH1460 1.3 31.5 1.0
C22 A:WVH1460 2.3 33.3 1.0
C8 A:WVH1460 2.4 29.4 1.0
N2 A:WVH1460 3.0 31.6 1.0
C7 A:WVH1460 3.0 29.4 1.0
CE1 A:TYR103 3.4 50.3 1.0
C11 A:WVH1460 3.6 38.5 1.0
C9 A:WVH1460 3.6 29.8 1.0
CD1 A:ILE105 3.8 37.1 1.0
CE A:MET460 3.9 33.8 1.0
CD1 A:TYR103 3.9 47.5 1.0
C26 A:WVH1460 3.9 48.0 1.0
C10 A:WVH1460 4.1 34.9 1.0
O A:HOH2029 4.1 37.5 1.0
O A:WVH1460 4.2 35.5 1.0
C6 A:WVH1460 4.3 32.5 1.0
C24 A:WVH1460 4.6 36.7 1.0
CZ A:TYR103 4.6 46.4 1.0
CG1 A:ILE105 4.7 34.8 1.0
C25 A:WVH1460 4.7 37.9 1.0
N3 A:WVH1460 4.7 47.4 1.0
OH A:TYR103 4.7 49.9 1.0
SD A:MET106 4.9 31.6 1.0
N5 A:WVH1460 5.0 50.5 1.0
C12 A:WVH1460 5.0 47.2 1.0

Fluorine binding site 2 out of 3 in 4c0c

Go back to Fluorine Binding Sites List in 4c0c
Fluorine binding site 2 out of 3 in the Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(2,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(2,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1460

b:46.8
occ:1.00
 F1 A:WVH1460 0.0 46.8 1.0
C19 A:WVH1460 1.3 40.7 1.0
C18 A:WVH1460 2.3 47.9 1.0
C14 A:WVH1460 2.4 40.2 1.0
N4 A:WVH1460 2.8 36.9 1.0
C20 A:WVH1460 3.1 34.8 1.0
CD2 A:PHE48 3.5 54.8 1.0
C17 A:WVH1460 3.6 46.5 1.0
CG A:PHE48 3.6 50.1 1.0
C15 A:WVH1460 3.7 38.5 1.0
CB A:PHE48 3.7 46.3 1.0
CG2 A:ILE45 3.8 40.4 1.0
C13 A:WVH1460 3.9 43.2 1.0
C21 A:WVH1460 4.1 41.7 1.0
C16 A:WVH1460 4.1 41.7 1.0
CE2 A:PHE48 4.3 54.5 1.0
CE2 A:PHE214 4.3 31.9 1.0
CG1 A:ILE45 4.3 34.3 1.0
CB A:ILE45 4.5 35.2 1.0
CA A:ILE45 4.5 31.3 1.0
CD1 A:PHE48 4.5 51.4 1.0
F A:WVH1460 4.6 65.9 1.0
CZ A:PHE214 4.8 28.9 1.0
O A:ILE45 4.9 32.9 1.0
C12 A:WVH1460 5.0 47.2 1.0

Fluorine binding site 3 out of 3 in 4c0c

Go back to Fluorine Binding Sites List in 4c0c
Fluorine binding site 3 out of 3 in the Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(2,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(2,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1460

b:65.9
occ:1.00
 F A:WVH1460 0.0 65.9 1.0
C17 A:WVH1460 1.4 46.5 1.0
C18 A:WVH1460 2.3 47.9 1.0
C16 A:WVH1460 2.5 41.7 1.0
C19 A:WVH1460 3.6 40.7 1.0
CD1 A:ILE72 3.6 34.1 1.0
CD1 A:ILE70 3.6 48.0 1.0
C15 A:WVH1460 3.7 38.5 1.0
CD1 A:PHE48 3.8 51.4 1.0
CE1 A:PHE48 4.0 51.5 1.0
C14 A:WVH1460 4.2 40.2 1.0
CE A:MET358 4.4 56.2 1.0
CG A:PHE48 4.4 50.1 1.0
F1 A:WVH1460 4.6 46.8 1.0
CD1 A:ILE79 4.7 37.2 1.0
CG1 A:VAL77 4.8 30.7 1.0
CG1 A:ILE70 4.8 43.4 1.0
CZ A:PHE48 4.8 52.5 1.0
CE2 A:PHE55 4.8 44.1 1.0
CZ A:PHE214 4.9 28.9 1.0
CB A:PHE48 4.9 46.3 1.0
CG1 A:ILE72 5.0 30.4 1.0

Reference:

C.M.Calvet, D.F.Vieira, J.Y.Choi, D.Kellar, M.D.Cameron, J.L.Siqueira-Neto, J.Gut, J.B.Johnston, L.Lin, S.Khan, J.H.Mckerrow, W.R.Roush, L.M.Podust. 4-Aminopyridyl-Based CYP51 Inhibitors As Anti-Trypanosoma Cruzi Drug Leads with Improved Pharmacokinetic Profile and in Vivo Potency. J.Med.Chem. V. 57 6989 2014.
ISSN: ISSN 0022-2623
PubMed: 25101801
DOI: 10.1021/JM500448U
Page generated: Thu Aug 1 00:27:33 2024

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