Fluorine in PDB 8fgt: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine

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

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

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine, PDB code: 8fgt 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) 39.74 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.464, 151.536, 107.479, 90, 90.48, 90
R / Rfree (%) 19.9 / 24.1

Other elements in 8fgt:

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

Zinc (Zn) 2 atoms
Chlorine (Cl) 4 atoms
Iron (Fe) 4 atoms
Gadolinium (Gd) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine (pdb code 8fgt). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine, PDB code: 8fgt:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 8fgt

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Fluorine binding site 1 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-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 Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:126.8
occ:1.00
 F12 A:XVK504 0.0 126.8 1.0
C12 A:XVK504 1.3 128.1 1.0
C11 A:XVK504 2.4 121.7 1.0
C13 A:XVK504 2.4 135.2 1.0
F13 A:XVK504 2.7 144.5 1.0
C09 A:XVK504 2.8 108.9 1.0
C05 A:XVK504 3.2 75.6 1.0
CG2 A:VAL336 3.2 52.8 1.0
C4D A:HEM501 3.4 46.2 1.0
C08 A:XVK504 3.4 93.2 1.0
CBD A:HEM501 3.5 71.2 1.0
C3D A:HEM501 3.5 58.3 1.0
C06 A:XVK504 3.5 78.3 1.0
CE1 A:PHE353 3.6 52.8 1.0
C16 A:XVK504 3.6 124.2 1.0
C14 A:XVK504 3.6 130.2 1.0
ND A:HEM501 3.6 40.9 1.0
CHA A:HEM501 3.7 41.5 1.0
CZ A:PHE353 3.8 51.2 1.0
C2D A:HEM501 3.8 53.6 1.0
C1D A:HEM501 3.9 49.7 1.0
CB A:VAL336 4.1 54.4 1.0
C04 A:XVK504 4.1 66.7 1.0
C15 A:XVK504 4.1 123.9 1.0
CAD A:HEM501 4.1 63.4 1.0
CG1 A:VAL336 4.5 54.1 1.0
C1A A:HEM501 4.5 45.6 1.0
C07 A:XVK504 4.5 65.1 1.0
CGD A:HEM501 4.6 71.4 1.0
N01 A:XVK504 4.6 62.8 1.0
O2D A:HEM501 4.8 72.1 1.0
CHD A:HEM501 4.8 48.7 1.0
CMD A:HEM501 4.8 47.6 1.0
CD1 A:PHE353 4.8 53.6 1.0
FE A:HEM501 4.9 40.8 1.0
CBA A:HEM501 4.9 62.9 1.0
SD A:MET339 5.0 57.4 1.0
NA A:HEM501 5.0 45.5 1.0

Fluorine binding site 2 out of 8 in 8fgt

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Fluorine binding site 2 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-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 Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:144.5
occ:1.00
 F13 A:XVK504 0.0 144.5 1.0
C13 A:XVK504 1.3 135.2 1.0
C12 A:XVK504 2.4 128.1 1.0
C14 A:XVK504 2.4 130.2 1.0
SD A:MET339 2.5 57.4 1.0
F12 A:XVK504 2.7 126.8 1.0
CG1 A:VAL336 3.1 54.1 1.0
CZ A:PHE353 3.3 51.2 1.0
CG A:MET339 3.4 55.2 1.0
CBD A:HEM501 3.5 71.2 1.0
C15 A:XVK504 3.6 123.9 1.0
C11 A:XVK504 3.6 121.7 1.0
CG2 A:VAL336 3.6 52.8 1.0
CB A:VAL336 3.7 54.4 1.0
CGD A:HEM501 3.9 71.4 1.0
O2D A:HEM501 3.9 72.1 1.0
CE1 A:PHE353 4.0 52.8 1.0
C16 A:XVK504 4.1 124.2 1.0
CE A:MET339 4.1 58.0 1.0
CE2 A:PHE353 4.2 53.6 1.0
CAD A:HEM501 4.3 63.4 1.0
C3D A:HEM501 4.3 58.3 1.0
C2D A:HEM501 4.4 53.6 1.0
CMD A:HEM501 4.4 47.6 1.0
CB A:MET339 4.5 55.0 1.0
O1D A:HEM501 4.6 65.1 1.0
OD1 A:ASN338 4.7 66.7 1.0
C09 A:XVK504 4.9 108.9 1.0
C17 A:XVK504 4.9 115.7 1.0
O A:HOH720 5.0 63.1 1.0

Fluorine binding site 3 out of 8 in 8fgt

Go back to Fluorine Binding Sites List in 8fgt
Fluorine binding site 3 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-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 Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:110.7
occ:1.00
 F12 B:XVK503 0.0 110.7 1.0
C12 B:XVK503 1.3 106.3 1.0
C13 B:XVK503 2.4 112.4 1.0
C11 B:XVK503 2.4 88.8 1.0
F13 B:XVK503 2.7 118.4 1.0
C09 B:XVK503 2.9 64.3 1.0
C05 B:XVK503 2.9 44.9 1.0
C4D B:HEM501 3.0 33.9 1.0
CHA B:HEM501 3.2 24.4 1.0
C06 B:XVK503 3.3 47.7 1.0
ND B:HEM501 3.3 33.8 1.0
C3D B:HEM501 3.4 30.8 1.0
C08 B:XVK503 3.5 39.1 1.0
CG2 B:VAL336 3.5 31.6 1.0
C04 B:XVK503 3.6 40.1 1.0
C14 B:XVK503 3.6 110.0 1.0
C16 B:XVK503 3.6 93.7 1.0
CBD B:HEM501 3.7 52.6 1.0
C1A B:HEM501 3.8 31.4 1.0
C1D B:HEM501 3.8 35.9 1.0
C2D B:HEM501 3.9 35.4 1.0
CE1 B:PHE353 4.1 29.9 1.0
C15 B:XVK503 4.1 102.6 1.0
C07 B:XVK503 4.1 29.2 1.0
N01 B:XVK503 4.2 38.0 1.0
CAD B:HEM501 4.2 35.0 1.0
NA B:HEM501 4.3 36.8 1.0
CBA B:HEM501 4.4 44.4 1.0
FE B:HEM501 4.4 32.1 1.0
C03 B:XVK503 4.5 30.3 1.0
CZ B:PHE353 4.6 34.3 1.0
CB B:VAL336 4.6 30.1 1.0
C02 B:XVK503 4.7 33.9 1.0
C2A B:HEM501 4.7 29.5 1.0
CHD B:HEM501 4.7 27.7 1.0
CGD B:HEM501 4.8 59.5 1.0
NC B:HEM501 5.0 26.0 1.0
O2D B:HEM501 5.0 44.1 1.0

Fluorine binding site 4 out of 8 in 8fgt

Go back to Fluorine Binding Sites List in 8fgt
Fluorine binding site 4 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-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 Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:118.4
occ:1.00
 F13 B:XVK503 0.0 118.4 1.0
C13 B:XVK503 1.3 112.4 1.0
C14 B:XVK503 2.4 110.0 1.0
C12 B:XVK503 2.4 106.3 1.0
F12 B:XVK503 2.7 110.7 1.0
SD B:MET339 3.0 38.3 1.0
CZ B:PHE353 3.1 34.3 1.0
CBD B:HEM501 3.2 52.6 1.0
C3D B:HEM501 3.4 30.8 1.0
C2D B:HEM501 3.4 35.4 1.0
CAD B:HEM501 3.5 35.0 1.0
CG1 B:VAL336 3.6 28.9 1.0
CE1 B:PHE353 3.6 29.9 1.0
C15 B:XVK503 3.6 102.6 1.0
C11 B:XVK503 3.6 88.8 1.0
CMD B:HEM501 3.7 28.4 1.0
CG2 B:VAL336 3.7 31.6 1.0
CGD B:HEM501 3.8 59.5 1.0
O2D B:HEM501 3.9 44.1 1.0
CB B:VAL336 3.9 30.1 1.0
C4D B:HEM501 4.0 33.9 1.0
C16 B:XVK503 4.1 93.7 1.0
C1D B:HEM501 4.1 35.9 1.0
CG B:MET339 4.2 27.5 1.0
CE2 B:PHE353 4.3 40.2 1.0
CE B:MET339 4.4 29.3 1.0
ND B:HEM501 4.5 33.8 1.0
O1D B:HEM501 4.6 71.9 1.0
CHA B:HEM501 4.8 24.4 1.0
C17 B:XVK503 4.9 101.5 1.0
C09 B:XVK503 4.9 64.3 1.0
CHD B:HEM501 4.9 27.7 1.0
CD1 B:PHE353 5.0 32.5 1.0

Fluorine binding site 5 out of 8 in 8fgt

Go back to Fluorine Binding Sites List in 8fgt
Fluorine binding site 5 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-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 5 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F503

b:128.1
occ:1.00
 F12 C:XVK503 0.0 128.1 1.0
C12 C:XVK503 1.3 124.8 1.0
C11 C:XVK503 2.4 110.1 1.0
C13 C:XVK503 2.4 132.6 1.0
F13 C:XVK503 2.7 140.8 1.0
C09 C:XVK503 2.8 87.8 1.0
C05 C:XVK503 3.2 57.1 1.0
CG2 C:VAL336 3.2 52.0 1.0
CBD C:HEM501 3.4 53.0 1.0
C08 C:XVK503 3.5 70.8 1.0
C06 C:XVK503 3.5 61.9 1.0
C4D C:HEM501 3.6 43.5 1.0
C16 C:XVK503 3.6 117.7 1.0
C14 C:XVK503 3.6 128.1 1.0
C3D C:HEM501 3.7 44.2 1.0
CHA C:HEM501 3.8 31.4 1.0
ND C:HEM501 4.0 37.9 1.0
CE1 C:PHE353 4.1 52.6 1.0
CAD C:HEM501 4.1 41.1 1.0
C04 C:XVK503 4.1 55.4 1.0
C2D C:HEM501 4.1 35.5 1.0
C15 C:XVK503 4.1 122.1 1.0
CB C:VAL336 4.2 48.9 1.0
C1D C:HEM501 4.3 45.4 1.0
CGD C:HEM501 4.4 58.4 1.0
O2D C:HEM501 4.4 62.0 1.0
CZ C:PHE353 4.4 47.8 1.0
C1A C:HEM501 4.5 42.8 1.0
N01 C:XVK503 4.5 55.1 1.0
CG1 C:VAL336 4.5 50.9 1.0
C07 C:XVK503 4.6 62.9 1.0
CBA C:HEM501 4.7 55.5 1.0
CMD C:HEM501 5.0 33.3 1.0
C03 C:XVK503 5.0 49.1 1.0

Fluorine binding site 6 out of 8 in 8fgt

Go back to Fluorine Binding Sites List in 8fgt
Fluorine binding site 6 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-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 6 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F503

b:140.8
occ:1.00
 F13 C:XVK503 0.0 140.8 1.0
C13 C:XVK503 1.3 132.6 1.0
C14 C:XVK503 2.4 128.1 1.0
C12 C:XVK503 2.4 124.8 1.0
SD C:MET339 2.7 49.4 1.0
F12 C:XVK503 2.7 128.1 1.0
CG1 C:VAL336 3.1 50.9 1.0
CBD C:HEM501 3.5 53.0 1.0
O2D C:HEM501 3.5 62.0 1.0
CGD C:HEM501 3.6 58.4 1.0
CG C:MET339 3.6 44.1 1.0
C15 C:XVK503 3.6 122.1 1.0
CG2 C:VAL336 3.6 52.0 1.0
C11 C:XVK503 3.6 110.1 1.0
CZ C:PHE353 3.8 47.8 1.0
CB C:VAL336 3.8 48.9 1.0
CAD C:HEM501 4.0 41.1 1.0
C16 C:XVK503 4.1 117.7 1.0
CE C:MET339 4.3 47.8 1.0
C3D C:HEM501 4.3 44.2 1.0
CE1 C:PHE353 4.3 52.6 1.0
O1D C:HEM501 4.4 67.0 1.0
C2D C:HEM501 4.5 35.5 1.0
CMD C:HEM501 4.6 33.3 1.0
O C:HOH679 4.7 73.0 1.0
CE2 C:PHE353 4.8 55.8 1.0
OD1 C:ASN338 4.8 59.0 1.0
C17 C:XVK503 4.9 118.2 1.0
CB C:MET339 4.9 42.7 1.0
C09 C:XVK503 4.9 87.8 1.0

Fluorine binding site 7 out of 8 in 8fgt

Go back to Fluorine Binding Sites List in 8fgt
Fluorine binding site 7 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-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 7 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F503

b:99.4
occ:1.00
 F12 D:XVK503 0.0 99.4 1.0
C12 D:XVK503 1.3 99.8 1.0
C13 D:XVK503 2.4 107.0 1.0
C11 D:XVK503 2.4 81.7 1.0
F13 D:XVK503 2.7 109.4 1.0
C05 D:XVK503 2.7 41.5 1.0
C09 D:XVK503 2.8 56.7 1.0
C06 D:XVK503 3.0 40.0 1.0
C08 D:XVK503 3.2 43.8 1.0
C4D D:HEM501 3.5 34.4 1.0
C04 D:XVK503 3.5 38.9 1.0
CG2 D:VAL336 3.5 28.1 1.0
CHA D:HEM501 3.6 28.9 1.0
ND D:HEM501 3.6 32.6 1.0
C14 D:XVK503 3.6 106.5 1.0
C16 D:XVK503 3.6 89.2 1.0
N01 D:XVK503 3.8 35.7 1.0
C1A D:HEM501 4.0 29.8 1.0
C3D D:HEM501 4.0 35.5 1.0
CBD D:HEM501 4.1 37.9 1.0
C07 D:XVK503 4.1 26.5 1.0
C15 D:XVK503 4.1 101.7 1.0
CE1 D:PHE353 4.2 28.1 1.0
C1D D:HEM501 4.2 33.7 1.0
CBA D:HEM501 4.2 36.1 1.0
C03 D:XVK503 4.3 29.6 1.0
NA D:HEM501 4.4 24.1 1.0
C02 D:XVK503 4.4 34.0 1.0
C2D D:HEM501 4.4 33.9 1.0
FE D:HEM501 4.6 31.6 1.0
CB D:VAL336 4.6 23.1 1.0
CZ D:PHE353 4.6 31.3 1.0
CAD D:HEM501 4.7 34.3 1.0
C2A D:HEM501 4.8 34.3 1.0
O2A D:HEM501 4.9 52.4 1.0
CHD D:HEM501 5.0 26.2 1.0

Fluorine binding site 8 out of 8 in 8fgt

Go back to Fluorine Binding Sites List in 8fgt
Fluorine binding site 8 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-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 8 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin-1-Yl)Ethyl) Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F503

b:109.4
occ:1.00
 F13 D:XVK503 0.0 109.4 1.0
C13 D:XVK503 1.3 107.0 1.0
C12 D:XVK503 2.4 99.8 1.0
C14 D:XVK503 2.4 106.5 1.0
F12 D:XVK503 2.7 99.4 1.0
CBD D:HEM501 2.9 37.9 1.0
CZ D:PHE353 3.2 31.3 1.0
SD D:MET339 3.2 36.3 1.0
CG2 D:VAL336 3.6 28.1 1.0
CE1 D:PHE353 3.6 28.1 1.0
C11 D:XVK503 3.6 81.7 1.0
CG1 D:VAL336 3.6 25.7 1.0
C15 D:XVK503 3.6 101.7 1.0
C3D D:HEM501 3.7 35.5 1.0
C2D D:HEM501 3.7 33.9 1.0
CGD D:HEM501 3.8 55.5 1.0
CB D:VAL336 3.9 23.1 1.0
CAD D:HEM501 3.9 34.3 1.0
O2D D:HEM501 4.0 41.7 1.0
CMD D:HEM501 4.1 25.9 1.0
C16 D:XVK503 4.1 89.2 1.0
C4D D:HEM501 4.1 34.4 1.0
C1D D:HEM501 4.2 33.7 1.0
CE2 D:PHE353 4.4 38.2 1.0
ND D:HEM501 4.4 32.6 1.0
CG D:MET339 4.5 29.4 1.0
CE D:MET339 4.5 34.0 1.0
CHA D:HEM501 4.8 28.9 1.0
O1D D:HEM501 4.8 62.3 1.0
C09 D:XVK503 4.9 56.7 1.0
C17 D:XVK503 4.9 104.8 1.0
C05 D:XVK503 4.9 41.5 1.0
CHD D:HEM501 5.0 26.2 1.0

Reference:

D.Vasu, H.T.Do, H.Li, C.D.Hardy, A.Awasthi, T.L.Poulos, R.B.Silverman. Potent, Selective, and Membrane Permeable 2-Amino-4-Substituted Pyridine-Based Neuronal Nitric Oxide Synthase Inhibitors. J.Med.Chem. V. 66 9934 2023.
ISSN: ISSN 0022-2623
PubMed: 37433128
DOI: 10.1021/ACS.JMEDCHEM.3C00782
Page generated: Fri Aug 2 18:57:45 2024

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