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Fluorine in PDB 4by0: 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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide

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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide

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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide:
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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide, PDB code: 4by0 was solved by J.Y.Choi, C.M.Calvet, D.F.Vieira, S.S.Gunatilleke, M.D.Cameron, J.H.Mckerrow, L.M.Podust, W.R.Roush, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.16 / 3.10
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.167, 124.167, 119.839, 90.00, 90.00, 120.00
R / Rfree (%) 23.195 / 29.748

Other elements in 4by0:

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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide also contains other interesting chemical elements:

Iron (Fe) 2 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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide (pdb code 4by0). 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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide, PDB code: 4by0:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4by0

Go back to Fluorine Binding Sites List in 4by0
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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide


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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1460

b:0.7
occ:1.00
 F1 A:5PS1460 0.0 0.7 1.0
C17 A:5PS1460 1.3 81.9 1.0
C18 A:5PS1460 2.3 77.1 1.0
C16 A:5PS1460 2.4 77.3 1.0
CG2 A:VAL213 3.4 82.7 1.0
C13 A:5PS1460 3.6 72.4 1.0
C15 A:5PS1460 3.6 76.7 1.0
CG1 A:VAL213 3.8 77.5 1.0
C14 A:5PS1460 4.1 78.9 1.0
CB A:VAL213 4.2 83.0 1.0
O A:PRO210 4.2 89.1 1.0
N A:VAL213 4.3 92.0 1.0
CE A:MET360 4.8 95.0 1.0
CA A:VAL213 4.8 85.3 1.0
C12 A:5PS1460 4.8 65.3 1.0
CB A:PRO210 4.9 85.2 1.0
CB A:ALA212 4.9 78.4 1.0
N A:ALA212 5.0 94.3 1.0

Fluorine binding site 2 out of 4 in 4by0

Go back to Fluorine Binding Sites List in 4by0
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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide


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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1460

b:61.0
occ:1.00
 F2 A:5PS1460 0.0 61.0 1.0
C20 A:5PS1460 1.3 64.3 1.0
C19 A:5PS1460 2.4 64.9 1.0
C9 A:5PS1460 2.4 66.7 1.0
C8 A:5PS1460 2.9 70.0 1.0
N3 A:5PS1460 2.9 66.2 1.0
C10 A:5PS1460 3.6 67.9 1.0
C12 A:5PS1460 3.6 65.3 1.0
C23 A:5PS1460 3.9 59.9 1.0
O1 A:5PS1460 3.9 76.6 1.0
C11 A:5PS1460 4.1 66.4 1.0
C7 A:5PS1460 4.2 63.1 1.0
C22 A:5PS1460 4.6 61.0 1.0
C21 A:5PS1460 4.6 62.5 1.0
N4 A:5PS1460 4.8 62.5 1.0
C13 A:5PS1460 4.9 72.4 1.0

Fluorine binding site 3 out of 4 in 4by0

Go back to Fluorine Binding Sites List in 4by0
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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide


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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1460

b:0.6
occ:1.00
 F1 B:5PS1460 0.0 0.6 1.0
C17 B:5PS1460 1.3 95.9 1.0
C16 B:5PS1460 2.3 93.5 1.0
C18 B:5PS1460 2.4 89.7 1.0
C15 B:5PS1460 3.6 95.4 1.0
C13 B:5PS1460 3.6 83.5 1.0
O B:PRO210 3.9 66.6 1.0
N B:ALA212 4.0 85.1 1.0
CB B:ALA212 4.1 70.6 1.0
C14 B:5PS1460 4.1 91.1 1.0
N B:VAL213 4.5 87.8 1.0
CA B:ALA212 4.6 76.5 1.0
C B:PRO210 4.6 69.7 1.0
CA B:ALA211 4.7 76.0 1.0
C B:ALA211 4.8 81.2 1.0
SD B:MET360 4.8 86.0 1.0
C12 B:5PS1460 4.9 76.0 1.0

Fluorine binding site 4 out of 4 in 4by0

Go back to Fluorine Binding Sites List in 4by0
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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide


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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1460

b:80.3
occ:1.00
 F2 B:5PS1460 0.0 80.3 1.0
C20 B:5PS1460 1.3 72.5 1.0
C19 B:5PS1460 2.3 73.1 1.0
C9 B:5PS1460 2.4 73.2 1.0
C8 B:5PS1460 2.9 76.6 1.0
N3 B:5PS1460 3.0 73.7 1.0
C12 B:5PS1460 3.6 76.0 1.0
C23 B:5PS1460 3.6 77.3 1.0
C10 B:5PS1460 3.7 70.5 1.0
CE B:MET460 3.8 77.3 1.0
O1 B:5PS1460 3.8 81.9 1.0
C11 B:5PS1460 4.1 73.2 1.0
C7 B:5PS1460 4.3 73.2 1.0
C22 B:5PS1460 4.4 76.4 1.0
C21 B:5PS1460 4.4 74.9 1.0
O B:HOH2001 4.6 46.0 1.0
N4 B:5PS1460 4.6 78.3 1.0
CE1 B:TYR103 4.7 96.3 1.0
C13 B:5PS1460 4.8 83.5 1.0
CZ B:TYR103 5.0 97.7 1.0
CD1 B:TYR103 5.0 91.5 1.0

Reference:

J.Y.Choi, C.M.Calvet, D.F.Vieira, S.S.Gunatilleke, M.D.Cameron, J.H.Mckerrow, L.M.Podust, W.R.Roush. R-Configuration of 4-Aminopyridyl-Based Inhibitors of CYP51 Confers Superior Efficacy Against Trypanosoma Cruzi Acs Med.Chem.Lett. V. 5 434 2014.
ISSN: ISSN 1948-5875
PubMed: 24900854
DOI: 10.1021/ML500010M
Page generated: Thu Aug 1 00:26:58 2024

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