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Fluorine in PDB 6ngy: Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(2,3-Difluoro-5-(2-(1-Methylpyrrolidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine

Enzymatic activity of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(2,3-Difluoro-5-(2-(1-Methylpyrrolidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine

All present enzymatic activity of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(2,3-Difluoro-5-(2-(1-Methylpyrrolidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(2,3-Difluoro-5-(2-(1-Methylpyrrolidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine, PDB code: 6ngy was solved by H.Li, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.00 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.843, 111.110, 164.285, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 23

Other elements in 6ngy:

The structure of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(2,3-Difluoro-5-(2-(1-Methylpyrrolidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(2,3-Difluoro-5-(2-(1-Methylpyrrolidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine (pdb code 6ngy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(2,3-Difluoro-5-(2-(1-Methylpyrrolidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine, PDB code: 6ngy:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6ngy

Go back to Fluorine Binding Sites List in 6ngy
Fluorine binding site 1 out of 4 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(2,3-Difluoro-5-(2-(1-Methylpyrrolidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(2,3-Difluoro-5-(2-(1-Methylpyrrolidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:0.5
occ:1.00
 F12 A:KN4803 0.0 0.5 1.0
C12 A:KN4803 1.3 0.6 1.0
C13 A:KN4803 2.3 0.6 1.0
C11 A:KN4803 2.4 91.9 1.0
F13 A:KN4803 2.7 0.0 1.0
C09 A:KN4803 2.8 75.3 1.0
C4D A:HEM801 3.0 40.0 1.0
ND A:HEM801 3.0 36.4 1.0
C05 A:KN4803 3.2 52.2 1.0
C08 A:KN4803 3.3 67.7 1.0
C3D A:HEM801 3.4 42.2 1.0
C1D A:HEM801 3.4 45.1 1.0
CHA A:HEM801 3.4 35.5 1.0
CG2 A:VAL567 3.4 37.5 1.0
C06 A:KN4803 3.5 63.3 1.0
C2D A:HEM801 3.6 44.2 1.0
C14 A:KN4803 3.6 0.7 1.0
C16 A:KN4803 3.6 95.3 1.0
CE1 A:PHE584 3.9 39.3 1.0
C1A A:HEM801 4.0 38.8 1.0
C15 A:KN4803 4.1 97.9 1.0
C04 A:KN4803 4.1 44.5 1.0
CHD A:HEM801 4.2 42.8 1.0
CAD A:HEM801 4.3 48.6 1.0
CZ A:PHE584 4.3 40.4 1.0
NA A:HEM801 4.3 39.6 1.0
FE A:HEM801 4.3 40.3 1.0
CB A:VAL567 4.4 39.8 1.0
CBD A:HEM801 4.5 54.6 1.0
N01 A:KN4803 4.5 56.0 1.0
C07 A:KN4803 4.6 46.3 1.0
C4C A:HEM801 4.7 38.3 1.0
NC A:HEM801 4.7 36.3 1.0
CMD A:HEM801 4.7 38.4 1.0
CG1 A:VAL567 4.8 45.6 1.0

Fluorine binding site 2 out of 4 in 6ngy

Go back to Fluorine Binding Sites List in 6ngy
Fluorine binding site 2 out of 4 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(2,3-Difluoro-5-(2-(1-Methylpyrrolidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(2,3-Difluoro-5-(2-(1-Methylpyrrolidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:0.0
occ:1.00
 F13 A:KN4803 0.0 0.0 1.0
C13 A:KN4803 1.3 0.6 1.0
C12 A:KN4803 2.3 0.6 1.0
C14 A:KN4803 2.4 0.7 1.0
F12 A:KN4803 2.7 0.5 1.0
SD A:MET570 3.0 61.9 1.0
CBD A:HEM801 3.2 54.6 1.0
CZ A:PHE584 3.4 40.4 1.0
C2D A:HEM801 3.5 44.2 1.0
C3D A:HEM801 3.5 42.2 1.0
C11 A:KN4803 3.6 91.9 1.0
CG1 A:VAL567 3.6 45.6 1.0
C15 A:KN4803 3.6 97.9 1.0
CMD A:HEM801 3.7 38.4 1.0
CAD A:HEM801 3.8 48.6 1.0
CG2 A:VAL567 3.8 37.5 1.0
CE1 A:PHE584 4.0 39.3 1.0
CG A:MET570 4.0 61.8 1.0
CB A:VAL567 4.1 39.8 1.0
C16 A:KN4803 4.1 95.3 1.0
C1D A:HEM801 4.2 45.1 1.0
C4D A:HEM801 4.2 40.0 1.0
CE2 A:PHE584 4.5 47.5 1.0
CGD A:HEM801 4.5 63.5 1.0
ND A:HEM801 4.5 36.4 1.0
CE A:MET570 4.6 68.9 1.0
C09 A:KN4803 4.8 75.3 1.0
C17 A:KN4803 4.8 98.3 1.0
CHD A:HEM801 4.9 42.8 1.0
CHA A:HEM801 4.9 35.5 1.0
O2D A:HEM801 5.0 68.8 1.0

Fluorine binding site 3 out of 4 in 6ngy

Go back to Fluorine Binding Sites List in 6ngy
Fluorine binding site 3 out of 4 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(2,3-Difluoro-5-(2-(1-Methylpyrrolidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(2,3-Difluoro-5-(2-(1-Methylpyrrolidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:0.2
occ:1.00
 F12 B:KN4803 0.0 0.2 1.0
C12 B:KN4803 1.4 0.9 1.0
C13 B:KN4803 2.3 0.0 1.0
C11 B:KN4803 2.4 85.8 1.0
F13 B:KN4803 2.7 0.9 1.0
C09 B:KN4803 2.8 61.6 1.0
C4D B:HEM801 3.2 39.8 1.0
ND B:HEM801 3.2 30.5 1.0
C3D B:HEM801 3.3 41.3 1.0
C1D B:HEM801 3.4 40.9 1.0
C05 B:KN4803 3.4 47.8 1.0
C2D B:HEM801 3.4 44.0 1.0
CG2 B:VAL567 3.4 38.1 1.0
CE1 B:PHE584 3.6 34.4 1.0
C14 B:KN4803 3.6 0.1 1.0
C08 B:KN4803 3.6 64.9 1.0
C16 B:KN4803 3.7 95.7 1.0
CHA B:HEM801 3.8 33.6 1.0
C06 B:KN4803 3.8 61.9 1.0
CZ B:PHE584 3.9 40.3 1.0
CBD B:HEM801 3.9 36.8 1.0
CHD B:HEM801 4.1 40.3 1.0
C15 B:KN4803 4.1 0.9 1.0
CAD B:HEM801 4.2 41.4 1.0
CB B:VAL567 4.2 35.7 1.0
C04 B:KN4803 4.3 42.4 1.0
CMD B:HEM801 4.3 36.8 1.0
C1A B:HEM801 4.4 46.9 1.0
CG1 B:VAL567 4.5 32.2 1.0
FE B:HEM801 4.5 40.7 1.0
C4C B:HEM801 4.6 42.9 1.0
C07 B:KN4803 4.6 45.6 1.0
NA B:HEM801 4.7 40.1 1.0
NC B:HEM801 4.8 43.7 1.0
CD1 B:PHE584 4.9 36.8 1.0
N01 B:KN4803 4.9 44.4 1.0

Fluorine binding site 4 out of 4 in 6ngy

Go back to Fluorine Binding Sites List in 6ngy
Fluorine binding site 4 out of 4 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(2,3-Difluoro-5-(2-(1-Methylpyrrolidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(2,3-Difluoro-5-(2-(1-Methylpyrrolidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:0.9
occ:1.00
 F13 B:KN4803 0.0 0.9 1.0
C13 B:KN4803 1.3 0.0 1.0
C12 B:KN4803 2.4 0.9 1.0
C14 B:KN4803 2.4 0.1 1.0
SD B:MET570 2.6 63.6 1.0
F12 B:KN4803 2.7 0.2 1.0
CBD B:HEM801 3.2 36.8 1.0
CG1 B:VAL567 3.4 32.2 1.0
CZ B:PHE584 3.5 40.3 1.0
C11 B:KN4803 3.6 85.8 1.0
C15 B:KN4803 3.6 0.9 1.0
CG B:MET570 3.8 47.2 1.0
CMD B:HEM801 3.9 36.8 1.0
C2D B:HEM801 4.0 44.0 1.0
C3D B:HEM801 4.0 41.3 1.0
CAD B:HEM801 4.0 41.4 1.0
CG2 B:VAL567 4.0 38.1 1.0
CB B:VAL567 4.1 35.7 1.0
CE B:MET570 4.1 76.3 1.0
C16 B:KN4803 4.1 95.7 1.0
CE1 B:PHE584 4.2 34.4 1.0
CGD B:HEM801 4.3 59.5 1.0
CE2 B:PHE584 4.5 38.5 1.0
O2D B:HEM801 4.7 68.5 1.0
C1D B:HEM801 4.7 40.9 1.0
CB B:MET570 4.7 36.2 1.0
C4D B:HEM801 4.7 39.8 1.0
C17 B:KN4803 4.8 0.6 1.0
C09 B:KN4803 4.8 61.6 1.0

Reference:

H.T.Do, H.Li, G.Chreifi, T.L.Poulos, R.B.Silverman. Optimization of Blood-Brain Barrier Permeability with Potent and Selective Human Neuronal Nitric Oxide Synthase Inhibitors Having A 2-Aminopyridine Scaffold. J. Med. Chem. V. 62 2690 2019.
ISSN: ISSN 1520-4804
PubMed: 30802056
DOI: 10.1021/ACS.JMEDCHEM.8B02032
Page generated: Thu Aug 1 22:54:05 2024

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