Fluorine in PDB 8fgl: Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin- 1-Yl)Ethyl)Phenethyl)-4-Methylpyridin-2-Amine, PDB code: 8fgl 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) 39.57 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.03, 121.912, 164.655, 90, 90.1, 90
R / Rfree (%) 21.5 / 28.1

Other elements in 8fgl:

The structure of Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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
Iron (Fe) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin- 1-Yl)Ethyl)Phenethyl)-4-Methylpyridin-2-Amine (pdb code 8fgl). 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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 6-(2,3-Difluoro-5-(2-(4-Methylpiperazin- 1-Yl)Ethyl)Phenethyl)-4-Methylpyridin-2-Amine, PDB code: 8fgl:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 8fgl

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Fluorine binding site 1 out of 8 in the Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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:F803

b:100.0
occ:1.00
 F12 A:XVK803 0.0 100.0 1.0
C12 A:XVK803 1.3 97.3 1.0
C13 A:XVK803 2.3 96.0 1.0
C11 A:XVK803 2.4 86.9 1.0
F13 A:XVK803 2.7 95.3 1.0
C09 A:XVK803 2.7 69.1 1.0
CG A:GLN483 3.1 65.7 1.0
OH A:TYR593 3.4 39.9 1.0
C14 A:XVK803 3.6 92.6 1.0
C16 A:XVK803 3.7 88.3 1.0
CB A:PRO570 3.7 39.5 1.0
CD A:GLN483 3.8 81.5 1.0
CA A:PRO570 3.8 36.6 1.0
O A:HOH935 4.0 54.5 1.0
C08 A:XVK803 4.1 54.9 1.0
N A:ALA571 4.1 41.7 1.0
C15 A:XVK803 4.1 89.7 1.0
CB A:GLN483 4.2 47.4 1.0
CZ A:TYR593 4.2 39.1 1.0
OE1 A:GLN483 4.3 88.0 1.0
OH A:TYR567 4.3 49.3 1.0
NE2 A:GLN483 4.3 86.1 1.0
C A:PRO570 4.3 40.6 1.0
CE2 A:TYR593 4.4 36.9 1.0
C06 A:XVK803 4.6 47.8 1.0
CE1 A:TYR567 4.7 51.2 1.0

Fluorine binding site 2 out of 8 in 8fgl

Go back to Fluorine Binding Sites List in 8fgl
Fluorine binding site 2 out of 8 in the Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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:F803

b:95.3
occ:1.00
 F13 A:XVK803 0.0 95.3 1.0
C13 A:XVK803 1.3 96.0 1.0
C12 A:XVK803 2.4 97.3 1.0
C14 A:XVK803 2.4 92.6 1.0
OH A:TYR567 2.5 49.3 1.0
F12 A:XVK803 2.7 100.0 1.0
CD A:ARG486 3.1 67.8 1.0
O A:HOH935 3.4 54.5 1.0
OH A:TYR593 3.6 39.9 1.0
NE A:ARG486 3.6 73.0 1.0
C11 A:XVK803 3.6 86.9 1.0
OE1 A:GLN483 3.6 88.0 1.0
C15 A:XVK803 3.7 89.7 1.0
NH1 A:ARG486 3.8 70.3 1.0
CZ A:TYR567 3.8 53.2 1.0
CG A:GLN483 3.9 65.7 1.0
CZ A:ARG486 3.9 73.0 1.0
CD A:GLN483 4.0 81.5 1.0
C16 A:XVK803 4.1 88.3 1.0
CE1 A:TYR567 4.3 51.2 1.0
CG A:ARG486 4.4 55.7 1.0
CB A:GLN483 4.4 47.4 1.0
O A:ILE485 4.6 44.6 1.0
CZ2 A:TRP566 4.7 36.8 1.0
C09 A:XVK803 4.8 69.1 1.0
CZ A:TYR593 4.8 39.1 1.0
NH2 A:ARG486 4.9 79.4 1.0
C17 A:XVK803 4.9 88.1 1.0
CE2 A:TYR567 4.9 46.0 1.0
OD1 A:ASP602 4.9 46.7 1.0
NE2 A:GLN483 5.0 86.1 1.0

Fluorine binding site 3 out of 8 in 8fgl

Go back to Fluorine Binding Sites List in 8fgl
Fluorine binding site 3 out of 8 in the Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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:F803

b:95.5
occ:1.00
 F12 B:XVK803 0.0 95.5 1.0
C12 B:XVK803 1.3 89.6 1.0
C13 B:XVK803 2.4 91.6 1.0
C11 B:XVK803 2.4 77.4 1.0
F13 B:XVK803 2.7 89.7 1.0
C09 B:XVK803 2.7 64.6 1.0
OH B:TYR593 3.4 38.8 1.0
CG B:GLN483 3.5 42.1 1.0
C14 B:XVK803 3.6 89.6 1.0
C16 B:XVK803 3.6 81.6 1.0
CA B:PRO570 3.8 42.4 1.0
CB B:PRO570 3.9 40.8 1.0
O B:HOH944 3.9 54.0 1.0
OH B:TYR567 4.0 55.6 1.0
N B:ALA571 4.1 36.9 1.0
CB B:GLN483 4.1 39.4 1.0
C15 B:XVK803 4.1 82.2 1.0
O B:HOH960 4.1 56.1 1.0
C08 B:XVK803 4.2 59.3 1.0
CZ B:TYR593 4.2 44.2 1.0
C B:PRO570 4.3 41.6 1.0
CD B:GLN483 4.3 62.0 1.0
CE1 B:TYR567 4.5 38.3 1.0
CE2 B:TYR593 4.5 40.4 1.0
NE2 B:GLN483 4.6 52.1 1.0
CZ B:TYR567 4.8 47.2 1.0
C06 B:XVK803 4.8 58.0 1.0
O B:HOH981 4.8 57.5 1.0

Fluorine binding site 4 out of 8 in 8fgl

Go back to Fluorine Binding Sites List in 8fgl
Fluorine binding site 4 out of 8 in the Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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:F803

b:89.7
occ:1.00
 F13 B:XVK803 0.0 89.7 1.0
C13 B:XVK803 1.4 91.6 1.0
C12 B:XVK803 2.4 89.6 1.0
C14 B:XVK803 2.4 89.6 1.0
OH B:TYR567 2.6 55.6 1.0
F12 B:XVK803 2.7 95.5 1.0
O B:HOH944 3.3 54.0 1.0
NE B:ARG486 3.3 65.4 1.0
CD B:ARG486 3.5 63.6 1.0
C11 B:XVK803 3.6 77.4 1.0
C15 B:XVK803 3.7 82.2 1.0
CZ B:ARG486 3.7 62.7 1.0
CG B:ARG486 3.8 60.1 1.0
OH B:TYR593 3.9 38.8 1.0
CZ B:TYR567 3.9 47.2 1.0
CG B:GLN483 4.1 42.1 1.0
NH1 B:ARG486 4.1 57.8 1.0
C16 B:XVK803 4.2 81.6 1.0
CD B:GLN483 4.2 62.0 1.0
NH2 B:ARG486 4.3 64.3 1.0
CE1 B:TYR567 4.4 38.3 1.0
OE1 B:GLN483 4.5 66.8 1.0
CB B:GLN483 4.5 39.4 1.0
O B:ILE485 4.6 46.6 1.0
NE2 B:GLN483 4.7 52.1 1.0
C09 B:XVK803 4.8 64.6 1.0
OD1 B:ASP602 4.8 54.5 1.0
C17 B:XVK803 4.9 72.7 1.0
CE2 B:TYR567 4.9 37.1 1.0
CB B:ARG486 5.0 45.1 1.0
CZ2 B:TRP566 5.0 29.8 1.0

Fluorine binding site 5 out of 8 in 8fgl

Go back to Fluorine Binding Sites List in 8fgl
Fluorine binding site 5 out of 8 in the Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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:F803

b:80.1
occ:1.00
 F12 C:XVK803 0.0 80.1 1.0
C12 C:XVK803 1.3 85.4 1.0
C13 C:XVK803 2.3 90.2 1.0
C11 C:XVK803 2.4 76.4 1.0
F13 C:XVK803 2.7 89.4 1.0
C09 C:XVK803 2.8 58.5 1.0
OH C:TYR593 3.1 37.8 1.0
CG C:GLN483 3.6 57.6 1.0
C14 C:XVK803 3.6 88.2 1.0
C16 C:XVK803 3.6 80.7 1.0
O C:HOH933 3.7 47.4 1.0
OH C:TYR567 3.9 54.9 1.0
CB C:PRO570 4.0 39.4 1.0
CZ C:TYR593 4.0 47.0 1.0
CA C:PRO570 4.1 40.2 1.0
C15 C:XVK803 4.1 80.8 1.0
O C:HOH969 4.2 65.2 1.0
CE2 C:TYR593 4.2 45.3 1.0
C08 C:XVK803 4.3 51.2 1.0
CB C:GLN483 4.3 52.3 1.0
CD C:GLN483 4.4 70.0 1.0
CE1 C:TYR567 4.5 43.4 1.0
N C:ALA571 4.6 48.0 1.0
O C:HOH940 4.6 51.1 1.0
CZ C:TYR567 4.7 49.6 1.0
C C:PRO570 4.8 43.2 1.0
NE2 C:GLN483 4.8 60.4 1.0
CD C:ARG486 4.9 60.9 1.0
C06 C:XVK803 4.9 54.1 1.0

Fluorine binding site 6 out of 8 in 8fgl

Go back to Fluorine Binding Sites List in 8fgl
Fluorine binding site 6 out of 8 in the Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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:F803

b:89.4
occ:1.00
 F13 C:XVK803 0.0 89.4 1.0
C13 C:XVK803 1.3 90.2 1.0
C12 C:XVK803 2.4 85.4 1.0
C14 C:XVK803 2.4 88.2 1.0
F12 C:XVK803 2.7 80.1 1.0
OH C:TYR567 2.9 54.9 1.0
CD C:ARG486 3.2 60.9 1.0
O C:HOH933 3.2 47.4 1.0
NH1 C:ARG486 3.4 60.2 1.0
NE C:ARG486 3.4 61.7 1.0
CZ C:ARG486 3.5 62.5 1.0
C11 C:XVK803 3.6 76.4 1.0
C15 C:XVK803 3.7 80.8 1.0
OH C:TYR593 3.9 37.8 1.0
CD C:GLN483 4.1 70.0 1.0
CG C:GLN483 4.1 57.6 1.0
C16 C:XVK803 4.2 80.7 1.0
OE1 C:GLN483 4.2 73.3 1.0
CZ C:TYR567 4.3 49.6 1.0
NH2 C:ARG486 4.3 62.1 1.0
OD1 C:ASP602 4.4 48.6 1.0
CG C:ARG486 4.6 50.9 1.0
NE2 C:GLN483 4.6 60.4 1.0
CZ2 C:TRP566 4.7 28.4 1.0
CB C:GLN483 4.7 52.3 1.0
C09 C:XVK803 4.8 58.5 1.0
CE1 C:TYR567 4.9 43.4 1.0
C17 C:XVK803 4.9 68.7 1.0
O C:HOH956 5.0 42.5 1.0

Fluorine binding site 7 out of 8 in 8fgl

Go back to Fluorine Binding Sites List in 8fgl
Fluorine binding site 7 out of 8 in the Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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:F803

b:90.8
occ:1.00
 F12 D:XVK803 0.0 90.8 1.0
C12 D:XVK803 1.3 90.2 1.0
C13 D:XVK803 2.3 93.3 1.0
C11 D:XVK803 2.4 80.2 1.0
F13 D:XVK803 2.6 95.8 1.0
C09 D:XVK803 2.8 60.2 1.0
OH D:TYR593 3.1 38.8 1.0
CG D:GLN483 3.2 68.8 1.0
C14 D:XVK803 3.6 90.5 1.0
C16 D:XVK803 3.7 79.8 1.0
O D:HOH920 3.7 54.2 1.0
OH D:TYR567 3.8 48.5 1.0
CA D:PRO570 3.9 39.8 1.0
CB D:PRO570 3.9 34.9 1.0
CD D:GLN483 3.9 82.0 1.0
CZ D:TYR593 4.0 46.9 1.0
CB D:GLN483 4.1 55.5 1.0
C15 D:XVK803 4.1 84.6 1.0
N D:ALA571 4.3 37.7 1.0
NE2 D:GLN483 4.4 78.1 1.0
C08 D:XVK803 4.4 52.5 1.0
CE1 D:TYR567 4.5 44.1 1.0
CE2 D:TYR593 4.5 47.4 1.0
C D:PRO570 4.6 39.0 1.0
OE1 D:GLN483 4.6 88.3 1.0
CZ D:TYR567 4.7 51.2 1.0
C06 D:XVK803 4.9 46.7 1.0
O D:ILE485 5.0 50.0 1.0

Fluorine binding site 8 out of 8 in 8fgl

Go back to Fluorine Binding Sites List in 8fgl
Fluorine binding site 8 out of 8 in the Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant 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:F803

b:95.8
occ:1.00
 F13 D:XVK803 0.0 95.8 1.0
C13 D:XVK803 1.4 93.3 1.0
C12 D:XVK803 2.3 90.2 1.0
C14 D:XVK803 2.4 90.5 1.0
F12 D:XVK803 2.6 90.8 1.0
OH D:TYR567 2.8 48.5 1.0
NE D:ARG486 3.3 66.5 1.0
CZ D:ARG486 3.5 64.9 1.0
OE1 D:GLN483 3.5 88.3 1.0
CD D:GLN483 3.6 82.0 1.0
C11 D:XVK803 3.6 80.2 1.0
CG D:GLN483 3.7 68.8 1.0
C15 D:XVK803 3.7 84.6 1.0
CD D:ARG486 3.7 67.7 1.0
O D:HOH920 3.9 54.2 1.0
CG D:ARG486 3.9 58.1 1.0
NH2 D:ARG486 4.0 67.5 1.0
NH1 D:ARG486 4.0 61.3 1.0
CB D:GLN483 4.1 55.5 1.0
CZ D:TYR567 4.1 51.2 1.0
OH D:TYR593 4.1 38.8 1.0
C16 D:XVK803 4.2 79.8 1.0
NE2 D:GLN483 4.4 78.1 1.0
O D:ILE485 4.4 50.0 1.0
CE1 D:TYR567 4.7 44.1 1.0
C09 D:XVK803 4.8 60.2 1.0
C17 D:XVK803 4.9 84.6 1.0
CB D:ARG486 5.0 49.1 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 18:50:14 2024

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