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

Enzymatic activity of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(2,3-Difluoro-5-(2-(1-Methylazetidin-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 (S)-6-(2,3-Difluoro-5-(2-(1-Methylazetidin-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 (S)-6-(2,3-Difluoro-5-(2-(1-Methylazetidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine, PDB code: 6nhd 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) 49.01 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.374, 111.227, 163.802, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 26

Other elements in 6nhd:

The structure of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(2,3-Difluoro-5-(2-(1-Methylazetidin-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 (S)-6-(2,3-Difluoro-5-(2-(1-Methylazetidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine (pdb code 6nhd). 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 (S)-6-(2,3-Difluoro-5-(2-(1-Methylazetidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine, PDB code: 6nhd:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6nhd

Go back to Fluorine Binding Sites List in 6nhd
Fluorine binding site 1 out of 4 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(2,3-Difluoro-5-(2-(1-Methylazetidin-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 (S)-6-(2,3-Difluoro-5-(2-(1-Methylazetidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:90.1
occ:1.00
 F12 A:KNV803 0.0 90.1 1.0
C12 A:KNV803 1.3 84.8 1.0
C11 A:KNV803 2.4 73.8 1.0
C13 A:KNV803 2.4 84.5 1.0
C09 A:KNV803 2.7 62.8 1.0
F13 A:KNV803 2.7 89.0 1.0
C4D A:HEM801 2.9 46.5 1.0
ND A:HEM801 2.9 41.2 1.0
C05 A:KNV803 3.2 48.6 1.0
C1D A:HEM801 3.2 45.9 1.0
C3D A:HEM801 3.3 48.8 1.0
CHA A:HEM801 3.4 40.7 1.0
C08 A:KNV803 3.4 60.5 1.0
C2D A:HEM801 3.5 45.0 1.0
C06 A:KNV803 3.5 57.7 1.0
C14 A:KNV803 3.6 83.5 1.0
C16 A:KNV803 3.6 79.6 1.0
CG2 A:VAL567 3.7 38.5 1.0
C1A A:HEM801 3.9 41.9 1.0
CE1 A:PHE584 4.0 51.8 1.0
CHD A:HEM801 4.1 49.5 1.0
C04 A:KNV803 4.1 47.6 1.0
C15 A:KNV803 4.1 83.2 1.0
NA A:HEM801 4.1 49.1 1.0
CAD A:HEM801 4.2 51.6 1.0
CZ A:PHE584 4.2 52.8 1.0
FE A:HEM801 4.2 46.8 1.0
CB A:VAL567 4.5 42.9 1.0
CBD A:HEM801 4.5 54.4 1.0
C07 A:KNV803 4.5 53.5 1.0
C4C A:HEM801 4.5 46.3 1.0
N01 A:KNV803 4.6 55.8 1.0
NC A:HEM801 4.6 51.1 1.0
CMD A:HEM801 4.6 46.1 1.0
CG1 A:VAL567 4.9 45.0 1.0
C2A A:HEM801 5.0 46.6 1.0

Fluorine binding site 2 out of 4 in 6nhd

Go back to Fluorine Binding Sites List in 6nhd
Fluorine binding site 2 out of 4 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(2,3-Difluoro-5-(2-(1-Methylazetidin-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 (S)-6-(2,3-Difluoro-5-(2-(1-Methylazetidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:89.0
occ:1.00
 F13 A:KNV803 0.0 89.0 1.0
C13 A:KNV803 1.3 84.5 1.0
C12 A:KNV803 2.4 84.8 1.0
C14 A:KNV803 2.4 83.5 1.0
F12 A:KNV803 2.7 90.1 1.0
SD A:MET570 2.9 68.0 1.0
CBD A:HEM801 3.3 54.4 1.0
C2D A:HEM801 3.4 45.0 1.0
CZ A:PHE584 3.4 52.8 1.0
C3D A:HEM801 3.5 48.8 1.0
CMD A:HEM801 3.6 46.1 1.0
C11 A:KNV803 3.6 73.8 1.0
C15 A:KNV803 3.6 83.2 1.0
CG1 A:VAL567 3.7 45.0 1.0
CAD A:HEM801 3.8 51.6 1.0
C1D A:HEM801 4.0 45.9 1.0
CG2 A:VAL567 4.1 38.5 1.0
CE1 A:PHE584 4.1 51.8 1.0
C16 A:KNV803 4.1 79.6 1.0
C4D A:HEM801 4.2 46.5 1.0
CB A:VAL567 4.2 42.9 1.0
CG A:MET570 4.2 63.2 1.0
CE A:MET570 4.4 71.3 1.0
CE2 A:PHE584 4.5 51.7 1.0
ND A:HEM801 4.5 41.2 1.0
CGD A:HEM801 4.6 62.7 1.0
CHD A:HEM801 4.7 49.5 1.0
C09 A:KNV803 4.8 62.8 1.0
C17 A:KNV803 4.8 90.4 1.0
CHA A:HEM801 4.9 40.7 1.0

Fluorine binding site 3 out of 4 in 6nhd

Go back to Fluorine Binding Sites List in 6nhd
Fluorine binding site 3 out of 4 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(2,3-Difluoro-5-(2-(1-Methylazetidin-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 (S)-6-(2,3-Difluoro-5-(2-(1-Methylazetidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:0.5
occ:1.00
 F12 B:KNV803 0.0 0.5 1.0
C12 B:KNV803 1.3 0.6 1.0
C11 B:KNV803 2.3 94.9 1.0
C13 B:KNV803 2.4 0.1 1.0
C09 B:KNV803 2.7 73.7 1.0
F13 B:KNV803 2.8 0.6 1.0
C05 B:KNV803 3.0 63.0 1.0
C4D B:HEM801 3.1 44.0 1.0
ND B:HEM801 3.1 42.9 1.0
C06 B:KNV803 3.3 67.6 1.0
C08 B:KNV803 3.3 71.0 1.0
CHA B:HEM801 3.5 44.9 1.0
CG2 B:VAL567 3.5 37.9 1.0
C1D B:HEM801 3.6 48.2 1.0
C16 B:KNV803 3.6 0.3 1.0
C14 B:KNV803 3.7 0.4 1.0
C3D B:HEM801 3.7 43.1 1.0
C04 B:KNV803 3.8 52.1 1.0
C1A B:HEM801 3.9 48.8 1.0
C2D B:HEM801 3.9 45.0 1.0
CE1 B:PHE584 4.0 38.2 1.0
NA B:HEM801 4.1 45.7 1.0
C15 B:KNV803 4.1 0.1 1.0
FE B:HEM801 4.2 42.0 1.0
CBD B:HEM801 4.2 44.7 1.0
N01 B:KNV803 4.3 56.6 1.0
CHD B:HEM801 4.4 45.8 1.0
C07 B:KNV803 4.4 44.0 1.0
CB B:VAL567 4.5 39.2 1.0
CAD B:HEM801 4.6 46.8 1.0
CZ B:PHE584 4.6 39.6 1.0
NC B:HEM801 4.7 53.6 1.0
C4C B:HEM801 4.7 54.0 1.0
C03 B:KNV803 4.7 52.8 1.0
C2A B:HEM801 4.8 59.8 1.0
C02 B:KNV803 4.9 47.4 1.0
CBA B:HEM801 4.9 64.8 1.0
CG1 B:VAL567 5.0 33.1 1.0

Fluorine binding site 4 out of 4 in 6nhd

Go back to Fluorine Binding Sites List in 6nhd
Fluorine binding site 4 out of 4 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(2,3-Difluoro-5-(2-(1-Methylazetidin-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 (S)-6-(2,3-Difluoro-5-(2-(1-Methylazetidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:0.6
occ:1.00
 F13 B:KNV803 0.0 0.6 1.0
C13 B:KNV803 1.3 0.1 1.0
C14 B:KNV803 2.4 0.4 1.0
C12 B:KNV803 2.4 0.6 1.0
F12 B:KNV803 2.8 0.5 1.0
SD B:MET570 3.0 64.0 1.0
CBD B:HEM801 3.2 44.7 1.0
CZ B:PHE584 3.4 39.6 1.0
CG1 B:VAL567 3.6 33.1 1.0
C15 B:KNV803 3.6 0.1 1.0
C11 B:KNV803 3.6 94.9 1.0
C3D B:HEM801 3.6 43.1 1.0
C2D B:HEM801 3.7 45.0 1.0
CG2 B:VAL567 3.7 37.9 1.0
CE1 B:PHE584 3.7 38.2 1.0
CAD B:HEM801 3.9 46.8 1.0
CMD B:HEM801 3.9 43.1 1.0
CB B:VAL567 4.0 39.2 1.0
C16 B:KNV803 4.1 0.3 1.0
CG B:MET570 4.2 51.4 1.0
C4D B:HEM801 4.2 44.0 1.0
C1D B:HEM801 4.2 48.2 1.0
CGD B:HEM801 4.3 60.0 1.0
CE B:MET570 4.4 63.0 1.0
ND B:HEM801 4.5 42.9 1.0
O2D B:HEM801 4.6 60.6 1.0
CE2 B:PHE584 4.6 39.0 1.0
C17 B:KNV803 4.9 0.7 1.0
C09 B:KNV803 4.9 73.7 1.0
CHD B:HEM801 4.9 45.8 1.0
CHA B:HEM801 4.9 44.9 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 23:00:47 2024

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