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Fluorine in PDB 6ngz: Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (S)-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 (S)-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 (S)-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 (S)-6-(2,3-Difluoro-5-(2-(1-Methylpyrrolidin-2-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine, PDB code: 6ngz 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) 48.88 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.620, 110.510, 163.500, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 24.4

Other elements in 6ngz:

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

Fluorine binding site 1 out of 4 in 6ngz

Go back to Fluorine Binding Sites List in 6ngz
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-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 (S)-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:0.9
occ:1.00
 F12 A:KPJ803 0.0 0.9 1.0
C12 A:KPJ803 1.4 93.6 1.0
C13 A:KPJ803 2.3 91.3 1.0
C11 A:KPJ803 2.4 80.6 1.0
F13 A:KPJ803 2.7 97.3 1.0
C09 A:KPJ803 2.7 66.2 1.0
C4D A:HEM801 3.0 35.6 1.0
ND A:HEM801 3.0 27.7 1.0
C05 A:KPJ803 3.1 42.3 1.0
C08 A:KPJ803 3.2 59.6 1.0
C06 A:KPJ803 3.3 56.0 1.0
CHA A:HEM801 3.4 34.6 1.0
CG2 A:VAL567 3.5 27.3 1.0
C1D A:HEM801 3.5 35.0 1.0
C3D A:HEM801 3.5 34.6 1.0
C14 A:KPJ803 3.6 85.4 1.0
C16 A:KPJ803 3.6 82.2 1.0
C2D A:HEM801 3.8 33.2 1.0
C1A A:HEM801 3.9 34.5 1.0
C04 A:KPJ803 4.0 38.7 1.0
CE1 A:PHE584 4.0 30.7 1.0
C15 A:KPJ803 4.1 83.2 1.0
NA A:HEM801 4.2 38.7 1.0
FE A:HEM801 4.2 40.8 1.0
CHD A:HEM801 4.3 32.4 1.0
N01 A:KPJ803 4.4 42.2 1.0
CB A:VAL567 4.4 36.7 1.0
CAD A:HEM801 4.4 37.1 1.0
CZ A:PHE584 4.4 31.6 1.0
C07 A:KPJ803 4.5 33.0 1.0
NC A:HEM801 4.6 29.9 1.0
CBD A:HEM801 4.7 45.5 1.0
C4C A:HEM801 4.7 27.2 1.0
CG1 A:VAL567 4.8 36.7 1.0
C2A A:HEM801 4.9 45.5 1.0
CMD A:HEM801 4.9 28.8 1.0
C03 A:KPJ803 4.9 38.7 1.0
CBA A:HEM801 4.9 60.8 1.0

Fluorine binding site 2 out of 4 in 6ngz

Go back to Fluorine Binding Sites List in 6ngz
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-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 (S)-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:97.3
occ:1.00
 F13 A:KPJ803 0.0 97.3 1.0
C13 A:KPJ803 1.3 91.3 1.0
C12 A:KPJ803 2.3 93.6 1.0
C14 A:KPJ803 2.3 85.4 1.0
F12 A:KPJ803 2.7 0.9 1.0
SD A:MET570 3.2 61.8 1.0
CBD A:HEM801 3.2 45.5 1.0
C2D A:HEM801 3.4 33.2 1.0
CZ A:PHE584 3.4 31.6 1.0
C3D A:HEM801 3.4 34.6 1.0
C15 A:KPJ803 3.6 83.2 1.0
C11 A:KPJ803 3.6 80.6 1.0
CG1 A:VAL567 3.7 36.7 1.0
CMD A:HEM801 3.7 28.8 1.0
CAD A:HEM801 3.8 37.1 1.0
CE1 A:PHE584 3.9 30.7 1.0
CG2 A:VAL567 3.9 27.3 1.0
C1D A:HEM801 4.0 35.0 1.0
C4D A:HEM801 4.0 35.6 1.0
C16 A:KPJ803 4.1 82.2 1.0
CB A:VAL567 4.1 36.7 1.0
CG A:MET570 4.1 55.6 1.0
ND A:HEM801 4.3 27.7 1.0
CE2 A:PHE584 4.5 43.1 1.0
CGD A:HEM801 4.6 52.0 1.0
CE A:MET570 4.7 69.1 1.0
CHD A:HEM801 4.7 32.4 1.0
CHA A:HEM801 4.8 34.6 1.0
C17 A:KPJ803 4.8 85.8 1.0
C09 A:KPJ803 4.8 66.2 1.0

Fluorine binding site 3 out of 4 in 6ngz

Go back to Fluorine Binding Sites List in 6ngz
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-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 (S)-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:1.0
occ:1.00
 F12 B:KPJ803 0.0 1.0 1.0
C12 B:KPJ803 1.4 95.7 1.0
C13 B:KPJ803 2.4 94.8 1.0
C11 B:KPJ803 2.4 82.7 1.0
F13 B:KPJ803 2.7 92.7 1.0
C09 B:KPJ803 2.8 61.6 1.0
C4D B:HEM801 3.1 33.2 1.0
ND B:HEM801 3.2 23.9 1.0
C3D B:HEM801 3.3 39.4 1.0
C1D B:HEM801 3.4 28.2 1.0
C05 B:KPJ803 3.4 47.4 1.0
CG2 B:VAL567 3.5 28.8 1.0
C2D B:HEM801 3.5 31.5 1.0
C08 B:KPJ803 3.6 53.8 1.0
CHA B:HEM801 3.6 29.9 1.0
C14 B:KPJ803 3.6 95.2 1.0
C16 B:KPJ803 3.6 91.6 1.0
CBD B:HEM801 3.8 38.5 1.0
C06 B:KPJ803 3.8 51.5 1.0
CE1 B:PHE584 3.8 28.0 1.0
CZ B:PHE584 4.1 32.7 1.0
CAD B:HEM801 4.1 36.6 1.0
C15 B:KPJ803 4.1 96.7 1.0
CHD B:HEM801 4.2 34.2 1.0
C1A B:HEM801 4.2 36.4 1.0
CB B:VAL567 4.3 28.9 1.0
C04 B:KPJ803 4.4 34.4 1.0
FE B:HEM801 4.4 32.8 1.0
CMD B:HEM801 4.4 26.4 1.0
NA B:HEM801 4.6 30.1 1.0
CG1 B:VAL567 4.6 25.8 1.0
C4C B:HEM801 4.7 31.6 1.0
C07 B:KPJ803 4.8 41.2 1.0
NC B:HEM801 4.8 36.1 1.0
N01 B:KPJ803 4.9 35.1 1.0

Fluorine binding site 4 out of 4 in 6ngz

Go back to Fluorine Binding Sites List in 6ngz
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-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 (S)-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:92.7
occ:1.00
 F13 B:KPJ803 0.0 92.7 1.0
C13 B:KPJ803 1.3 94.8 1.0
C12 B:KPJ803 2.4 95.7 1.0
C14 B:KPJ803 2.4 95.2 1.0
SD B:MET570 2.5 57.6 1.0
F12 B:KPJ803 2.7 1.0 1.0
CBD B:HEM801 3.4 38.5 1.0
CG1 B:VAL567 3.4 25.8 1.0
C11 B:KPJ803 3.6 82.7 1.0
CG B:MET570 3.6 31.8 1.0
C15 B:KPJ803 3.6 96.7 1.0
CZ B:PHE584 3.6 32.7 1.0
CG2 B:VAL567 3.9 28.8 1.0
C3D B:HEM801 4.0 39.4 1.0
C2D B:HEM801 4.0 31.5 1.0
CB B:VAL567 4.0 28.9 1.0
CAD B:HEM801 4.0 36.6 1.0
CMD B:HEM801 4.1 26.4 1.0
CE B:MET570 4.1 54.3 1.0
CGD B:HEM801 4.1 53.4 1.0
C16 B:KPJ803 4.1 91.6 1.0
CE1 B:PHE584 4.3 28.0 1.0
O2D B:HEM801 4.3 64.9 1.0
CB B:MET570 4.7 27.0 1.0
CE2 B:PHE584 4.7 32.9 1.0
C4D B:HEM801 4.7 33.2 1.0
C1D B:HEM801 4.7 28.2 1.0
C17 B:KPJ803 4.8 0.8 1.0
C09 B:KPJ803 4.8 61.6 1.0
O1D B:HEM801 4.9 40.9 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: Tue Jul 15 13:36:49 2025

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