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Fluorine in PDB 6ngx: Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(3-(Methylamino)Prop-1-Yn-1-Yl)Phenethyl)-4- Methylpyridin-2-Amine

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

All present enzymatic activity of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(3-(Methylamino)Prop-1-Yn-1-Yl)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 6-(2,3-Difluoro-5-(3-(Methylamino)Prop-1-Yn-1-Yl)Phenethyl)-4- Methylpyridin-2-Amine, PDB code: 6ngx 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 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.024, 111.008, 164.397, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.1

Other elements in 6ngx:

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

Fluorine binding site 1 out of 4 in 6ngx

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

b:95.9
occ:1.00
 F12 A:KMV803 0.0 95.9 1.0
C12 A:KMV803 1.3 98.6 1.0
C11 A:KMV803 2.3 87.8 1.0
C13 A:KMV803 2.4 0.8 1.0
C09 A:KMV803 2.7 68.1 1.0
F13 A:KMV803 2.7 0.8 1.0
CG2 A:VAL567 2.9 36.8 1.0
C08 A:KMV803 3.5 56.1 1.0
C16 A:KMV803 3.6 94.7 1.0
C14 A:KMV803 3.6 0.4 1.0
C05 A:KMV803 3.6 36.0 1.0
CB A:VAL567 3.7 42.2 1.0
CBD A:HEM801 3.7 57.9 1.0
C3D A:HEM801 3.7 38.6 1.0
C4D A:HEM801 3.7 36.5 1.0
CE1 A:PHE584 3.9 38.5 1.0
CG1 A:VAL567 3.9 44.0 1.0
C2D A:HEM801 3.9 34.9 1.0
ND A:HEM801 3.9 31.9 1.0
CZ A:PHE584 3.9 36.3 1.0
C06 A:KMV803 4.0 47.0 1.0
C1D A:HEM801 4.0 39.3 1.0
C15 A:KMV803 4.1 0.4 1.0
CHA A:HEM801 4.2 32.8 1.0
CAD A:HEM801 4.3 38.0 1.0
CMD A:HEM801 4.6 31.3 1.0
C04 A:KMV803 4.7 35.1 1.0
CHD A:HEM801 4.7 37.9 1.0
SD A:MET570 4.8 57.5 1.0
CGD A:HEM801 4.9 68.3 1.0
C1A A:HEM801 4.9 37.5 1.0

Fluorine binding site 2 out of 4 in 6ngx

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

b:0.8
occ:1.00
 F13 A:KMV803 0.0 0.8 1.0
C13 A:KMV803 1.3 0.8 1.0
C14 A:KMV803 2.4 0.4 1.0
C12 A:KMV803 2.4 98.6 1.0
F12 A:KMV803 2.7 95.9 1.0
SD A:MET570 2.8 57.5 1.0
CBD A:HEM801 3.2 57.9 1.0
CG1 A:VAL567 3.3 44.0 1.0
CG A:MET570 3.4 56.4 1.0
C15 A:KMV803 3.6 0.4 1.0
C11 A:KMV803 3.6 87.8 1.0
O2D A:HEM801 3.7 81.2 1.0
CGD A:HEM801 3.8 68.3 1.0
CE A:MET570 4.0 62.7 1.0
CG2 A:VAL567 4.1 36.8 1.0
C16 A:KMV803 4.1 94.7 1.0
CB A:VAL567 4.2 42.2 1.0
CZ A:PHE584 4.5 36.3 1.0
CAD A:HEM801 4.6 38.0 1.0
OD1 A:ASN569 4.6 48.4 1.0
C17 A:KMV803 4.6 1.0 1.0
C3D A:HEM801 4.8 38.6 1.0
CE2 A:TYR706 4.8 78.2 1.0
C09 A:KMV803 4.8 68.1 1.0
CB A:MET570 4.9 44.3 1.0
O1D A:HEM801 4.9 62.6 1.0
C2D A:HEM801 4.9 34.9 1.0
CMD A:HEM801 4.9 31.3 1.0

Fluorine binding site 3 out of 4 in 6ngx

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

b:0.3
occ:1.00
 F12 B:KMV803 0.0 0.3 1.0
C12 B:KMV803 1.3 0.5 1.0
C11 B:KMV803 2.4 95.9 1.0
C13 B:KMV803 2.4 0.7 1.0
C09 B:KMV803 2.7 74.3 1.0
F13 B:KMV803 2.7 0.8 1.0
CG2 B:VAL567 2.9 31.9 1.0
C08 B:KMV803 3.4 61.6 1.0
CBD B:HEM801 3.6 47.2 1.0
C14 B:KMV803 3.6 0.6 1.0
C16 B:KMV803 3.6 0.4 1.0
C05 B:KMV803 3.6 40.8 1.0
C4D B:HEM801 3.7 32.5 1.0
CB B:VAL567 3.8 31.9 1.0
C3D B:HEM801 3.8 38.0 1.0
CE1 B:PHE584 3.8 37.0 1.0
C06 B:KMV803 3.9 49.4 1.0
CG1 B:VAL567 3.9 35.9 1.0
ND B:HEM801 3.9 31.6 1.0
CZ B:PHE584 4.0 36.4 1.0
C2D B:HEM801 4.0 33.5 1.0
C1D B:HEM801 4.1 32.8 1.0
C15 B:KMV803 4.1 0.1 1.0
CHA B:HEM801 4.2 30.8 1.0
CAD B:HEM801 4.4 40.3 1.0
SD B:MET570 4.7 54.8 1.0
C04 B:KMV803 4.7 34.9 1.0
CGD B:HEM801 4.7 56.9 1.0
CMD B:HEM801 4.8 35.4 1.0
CHD B:HEM801 4.8 35.6 1.0
O2D B:HEM801 4.9 61.9 1.0
C1A B:HEM801 4.9 37.5 1.0

Fluorine binding site 4 out of 4 in 6ngx

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

b:0.8
occ:1.00
 F13 B:KMV803 0.0 0.8 1.0
C13 B:KMV803 1.3 0.7 1.0
C14 B:KMV803 2.4 0.6 1.0
C12 B:KMV803 2.4 0.5 1.0
SD B:MET570 2.5 54.8 1.0
F12 B:KMV803 2.7 0.3 1.0
CG1 B:VAL567 3.3 35.9 1.0
CG B:MET570 3.3 47.7 1.0
CBD B:HEM801 3.4 47.2 1.0
O2D B:HEM801 3.6 61.9 1.0
C15 B:KMV803 3.6 0.1 1.0
C11 B:KMV803 3.6 95.9 1.0
CGD B:HEM801 3.8 56.9 1.0
CE B:MET570 4.0 48.0 1.0
CG2 B:VAL567 4.0 31.9 1.0
O B:HOH1123 4.1 77.0 1.0
C16 B:KMV803 4.1 0.4 1.0
CB B:VAL567 4.2 31.9 1.0
CZ B:PHE584 4.3 36.4 1.0
OD1 B:ASN569 4.6 36.8 1.0
CAD B:HEM801 4.6 40.3 1.0
C17 B:KMV803 4.6 0.5 1.0
CB B:MET570 4.6 39.7 1.0
C3D B:HEM801 4.8 38.0 1.0
CE2 B:TYR706 4.8 61.8 1.0
O1D B:HEM801 4.8 55.5 1.0
C09 B:KMV803 4.8 74.3 1.0
C2D B:HEM801 4.9 33.5 1.0
CMD B:HEM801 5.0 35.4 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 13:35:40 2025

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