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Fluorine in PDB 4c28: 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-(4-Chlorophenyl)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-(4-Chlorophenyl)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-(4-Chlorophenyl)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-(4-Chlorophenyl)Piperazin-1-Yl)- 2-Fluorobenzamide., PDB code: 4c28 was solved by D.F.Vieira, C.M.Calvet, 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) 72.24 / 2.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.951, 79.005, 176.839, 90.00, 90.00, 90.00
R / Rfree (%) 18.574 / 23.761

Other elements in 4c28:

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-(4-Chlorophenyl)Piperazin-1-Yl)- 2-Fluorobenzamide. also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Chlorine (Cl) 5 atoms

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-(4-Chlorophenyl)Piperazin-1-Yl)- 2-Fluorobenzamide. (pdb code 4c28). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 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-(4-Chlorophenyl)Piperazin-1-Yl)- 2-Fluorobenzamide., PDB code: 4c28:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4c28

Go back to Fluorine Binding Sites List in 4c28
Fluorine binding site 1 out of 4 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-(4-Chlorophenyl)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-(4-Chlorophenyl)Piperazin-1-Yl)- 2-Fluorobenzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1460

b:28.7
occ:0.50
 F1 A:TW51460 0.0 28.7 0.5
F1 A:TW51460 0.1 28.2 0.5
C19 A:TW51460 1.3 22.0 0.5
C19 A:TW51460 1.3 22.6 0.5
C20 A:TW51460 2.3 22.7 0.5
C20 A:TW51460 2.3 23.2 0.5
C18 A:TW51460 2.4 21.2 0.5
C18 A:TW51460 2.5 21.8 0.5
N4 A:TW51460 2.7 18.7 0.5
N4 A:TW51460 2.8 17.7 0.5
C17 A:TW51460 2.9 19.5 0.5
C17 A:TW51460 3.0 20.2 0.5
C21 A:TW51460 3.6 21.8 0.5
C21 A:TW51460 3.6 22.2 0.5
C23 A:TW51460 3.6 21.4 0.5
C23 A:TW51460 3.7 22.0 0.5
C7 A:TW51460 3.9 18.9 0.5
C7 A:TW51460 4.1 17.8 0.5
CE1 A:TYR103 4.1 56.6 1.0
O2 A:TW51460 4.1 20.4 0.5
C22 A:TW51460 4.1 21.0 0.5
SD A:MET460 4.1 18.1 1.0
C22 A:TW51460 4.1 21.5 0.5
O2 A:TW51460 4.1 21.1 0.5
C8 A:TW51460 4.2 18.9 0.5
C16 A:TW51460 4.3 16.3 0.5
CD1 A:ILE105 4.3 22.6 1.0
C8 A:TW51460 4.4 17.4 0.5
CD1 A:TYR103 4.5 53.0 1.0
N5 A:TW51460 4.7 21.9 0.5
N5 A:TW51460 4.7 22.2 0.5
C9 A:TW51460 4.8 16.9 0.5
SD A:MET106 4.8 20.8 1.0
O A:HOH2050 4.8 30.2 1.0
CE A:MET460 5.0 18.3 1.0

Fluorine binding site 2 out of 4 in 4c28

Go back to Fluorine Binding Sites List in 4c28
Fluorine binding site 2 out of 4 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-(4-Chlorophenyl)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-(4-Chlorophenyl)Piperazin-1-Yl)- 2-Fluorobenzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1460

b:28.2
occ:0.50
 F1 A:TW51460 0.0 28.2 0.5
F1 A:TW51460 0.1 28.7 0.5
C19 A:TW51460 1.3 22.0 0.5
C19 A:TW51460 1.4 22.6 0.5
C20 A:TW51460 2.3 22.7 0.5
C20 A:TW51460 2.3 23.2 0.5
C18 A:TW51460 2.5 21.2 0.5
C18 A:TW51460 2.5 21.8 0.5
N4 A:TW51460 2.7 18.7 0.5
N4 A:TW51460 2.8 17.7 0.5
C17 A:TW51460 3.0 19.5 0.5
C17 A:TW51460 3.0 20.2 0.5
C21 A:TW51460 3.6 21.8 0.5
C21 A:TW51460 3.6 22.2 0.5
C23 A:TW51460 3.7 21.4 0.5
C23 A:TW51460 3.7 22.0 0.5
C7 A:TW51460 3.9 18.9 0.5
CE1 A:TYR103 4.0 56.6 1.0
C7 A:TW51460 4.1 17.8 0.5
C22 A:TW51460 4.1 21.0 0.5
O2 A:TW51460 4.1 20.4 0.5
C22 A:TW51460 4.1 21.5 0.5
O2 A:TW51460 4.2 21.1 0.5
C8 A:TW51460 4.2 18.9 0.5
SD A:MET460 4.2 18.1 1.0
C16 A:TW51460 4.3 16.3 0.5
CD1 A:ILE105 4.3 22.6 1.0
CD1 A:TYR103 4.4 53.0 1.0
C8 A:TW51460 4.4 17.4 0.5
C9 A:TW51460 4.7 16.9 0.5
N5 A:TW51460 4.8 21.9 0.5
N5 A:TW51460 4.8 22.2 0.5
SD A:MET106 4.8 20.8 1.0
O A:HOH2050 4.8 30.2 1.0
CG2 A:VAL213 5.0 20.6 1.0

Fluorine binding site 3 out of 4 in 4c28

Go back to Fluorine Binding Sites List in 4c28
Fluorine binding site 3 out of 4 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-(4-Chlorophenyl)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-(4-Chlorophenyl)Piperazin-1-Yl)- 2-Fluorobenzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1460

b:17.5
occ:0.50
 F1 B:TW51460 0.0 17.5 0.5
F1 B:TW51460 0.8 15.8 0.5
C19 B:TW51460 1.3 15.7 0.5
C19 B:TW51460 1.7 16.8 0.5
C20 B:TW51460 2.3 15.8 0.5
C18 B:TW51460 2.4 15.5 0.5
C18 B:TW51460 2.6 17.2 0.5
N4 B:TW51460 2.6 18.1 0.5
C20 B:TW51460 2.8 17.7 0.5
N4 B:TW51460 2.9 14.9 0.5
C17 B:TW51460 2.9 15.4 0.5
C17 B:TW51460 2.9 18.1 0.5
C21 B:TW51460 3.6 15.5 0.5
C23 B:TW51460 3.6 15.2 0.5
C7 B:TW51460 3.8 19.2 0.5
C23 B:TW51460 3.8 16.7 0.5
SD B:MET460 3.8 19.6 1.0
O2 B:TW51460 4.0 16.4 0.5
C21 B:TW51460 4.0 17.4 0.5
C7 B:TW51460 4.0 15.4 0.5
O2 B:TW51460 4.1 20.0 0.5
C22 B:TW51460 4.1 15.7 0.5
C8 B:TW51460 4.1 19.3 0.5
C8 B:TW51460 4.3 15.2 0.5
CE B:MET460 4.3 22.9 1.0
CE1 B:TYR103 4.3 42.6 1.0
C22 B:TW51460 4.4 17.2 0.5
CD1 B:ILE105 4.4 29.2 1.0
C16 B:TW51460 4.4 16.0 0.5
SD B:MET106 4.5 22.0 1.0
CD1 B:TYR103 4.5 43.1 1.0
C9 B:TW51460 4.8 15.6 0.5
N5 B:TW51460 4.8 15.0 0.5
CG B:MET460 4.9 17.5 1.0

Fluorine binding site 4 out of 4 in 4c28

Go back to Fluorine Binding Sites List in 4c28
Fluorine binding site 4 out of 4 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-(4-Chlorophenyl)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 4 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-(4-Chlorophenyl)Piperazin-1-Yl)- 2-Fluorobenzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1460

b:15.8
occ:0.50
 F1 B:TW51460 0.0 15.8 0.5
F1 B:TW51460 0.8 17.5 0.5
C19 B:TW51460 1.3 16.8 0.5
C19 B:TW51460 1.3 15.7 0.5
C20 B:TW51460 2.2 15.8 0.5
C20 B:TW51460 2.4 17.7 0.5
C18 B:TW51460 2.4 15.5 0.5
C18 B:TW51460 2.4 17.2 0.5
N4 B:TW51460 2.7 18.1 0.5
N4 B:TW51460 2.9 14.9 0.5
C17 B:TW51460 3.0 18.1 0.5
C17 B:TW51460 3.0 15.4 0.5
C21 B:TW51460 3.4 15.5 0.5
C23 B:TW51460 3.6 15.2 0.5
CE1 B:TYR103 3.6 42.6 1.0
C21 B:TW51460 3.6 17.4 0.5
C23 B:TW51460 3.7 16.7 0.5
CD1 B:TYR103 3.9 43.1 1.0
C22 B:TW51460 3.9 15.7 0.5
C7 B:TW51460 4.0 19.2 0.5
C22 B:TW51460 4.1 17.2 0.5
C8 B:TW51460 4.1 19.3 0.5
C16 B:TW51460 4.1 16.0 0.5
O2 B:TW51460 4.2 16.4 0.5
O2 B:TW51460 4.2 20.0 0.5
C7 B:TW51460 4.2 15.4 0.5
C8 B:TW51460 4.5 15.2 0.5
SD B:MET460 4.5 19.6 1.0
N5 B:TW51460 4.6 15.0 0.5
C9 B:TW51460 4.7 15.6 0.5
CD1 B:ILE105 4.7 29.2 1.0
CZ B:TYR103 4.7 42.1 1.0
O B:HOH2043 4.7 33.4 1.0
CG2 B:VAL213 4.8 23.5 1.0
N5 B:TW51460 4.8 16.9 0.5
SD B:MET106 4.8 22.0 1.0
C24 B:TW51460 4.9 15.6 0.5

Reference:

D.F.Vieira, C.M.Calvet, J.Y.Choi, M.D.Cameron, J.Gut, D.Kellar, J.L.Siqueira-Neto, J.H.Mckerrow, W.R.Roush, L.M.Podust. Orally Bioavailable N-Indolyl-Oxopyridinyl- 4AMINOPROPANYL CYP51 Inhibitors Are Highly Potent in the 4-Day Mouse Model of Trypanosoma Cruzi Infection To Be Published.
Page generated: Mon Jul 14 20:49:34 2025

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