Fluorine in PDB 8fgq: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine

Enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine

All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine, PDB code: 8fgq 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) 75.78 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.569, 151.48, 108.348, 90, 91.08, 90
R / Rfree (%) 19.3 / 24.6

Other elements in 8fgq:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine (pdb code 8fgq). 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 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine, PDB code: 8fgq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 8fgq

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

b:88.0
occ:1.00
 F11 A:V80503 0.0 88.0 1.0
C11 A:V80503 1.3 86.7 1.0
C12 A:V80503 2.3 89.0 1.0
C16 A:V80503 2.4 82.3 1.0
F12 A:V80503 2.7 91.3 1.0
C09 A:V80503 2.9 73.8 1.0
C08 A:V80503 2.9 62.1 1.0
CG2 A:VAL336 3.0 33.0 1.0
CBD A:HEM501 3.5 76.7 1.0
C13 A:V80503 3.6 90.6 1.0
C15 A:V80503 3.6 88.5 1.0
CGD A:HEM501 3.9 87.1 1.0
C06 A:V80503 3.9 54.0 1.0
C05 A:V80503 3.9 53.1 1.0
CG1 A:VAL336 3.9 50.7 1.0
CB A:VAL336 4.0 44.7 1.0
O2D A:HEM501 4.1 89.2 1.0
C14 A:V80503 4.1 95.4 1.0
C3D A:HEM501 4.4 59.5 1.0
CAD A:HEM501 4.5 63.8 1.0
C4D A:HEM501 4.5 51.1 1.0
O1D A:HEM501 4.6 94.7 1.0
CHA A:HEM501 4.7 45.2 1.0
O2A A:HEM501 4.7 94.6 1.0
SD A:MET339 4.8 50.6 1.0
CZ A:PHE353 4.8 38.3 1.0
CE1 A:PHE353 4.8 44.4 1.0
C2D A:HEM501 4.9 58.7 1.0
O A:HOH679 4.9 43.1 1.0

Fluorine binding site 2 out of 8 in 8fgq

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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 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-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 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:91.3
occ:1.00
 F12 A:V80503 0.0 91.3 1.0
C12 A:V80503 1.3 89.0 1.0
O2D A:HEM501 2.3 89.2 1.0
C11 A:V80503 2.4 86.7 1.0
C13 A:V80503 2.4 90.6 1.0
F11 A:V80503 2.7 88.0 1.0
CGD A:HEM501 3.0 87.1 1.0
CBD A:HEM501 3.3 76.7 1.0
C14 A:V80503 3.6 95.4 1.0
C16 A:V80503 3.6 82.3 1.0
SD A:MET339 3.9 50.6 1.0
O1D A:HEM501 4.0 94.7 1.0
CE1 A:TYR475 4.0 71.0 1.0
C15 A:V80503 4.1 88.5 1.0
O A:HOH706 4.5 44.8 1.0
CG1 A:VAL336 4.5 50.7 1.0
O A:HOH679 4.6 43.1 1.0
CG A:MET339 4.6 45.9 1.0
OH A:TYR475 4.7 63.6 1.0
O2A A:HEM501 4.8 94.6 1.0
CAD A:HEM501 4.8 63.8 1.0
CD1 A:TYR475 4.8 67.7 1.0
CZ A:TYR475 4.8 65.8 1.0
C17 A:V80503 4.9 102.6 1.0
C09 A:V80503 4.9 73.8 1.0
CG2 A:VAL336 4.9 33.0 1.0

Fluorine binding site 3 out of 8 in 8fgq

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Fluorine binding site 3 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-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 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:76.8
occ:1.00
 F11 B:V80503 0.0 76.8 1.0
C11 B:V80503 1.3 68.2 1.0
C12 B:V80503 2.4 75.8 1.0
C16 B:V80503 2.4 49.4 1.0
F12 B:V80503 2.8 83.8 1.0
C09 B:V80503 2.9 32.9 1.0
C08 B:V80503 2.9 24.3 1.0
CBD B:HEM501 3.1 54.6 1.0
O2D B:HEM501 3.2 81.1 1.0
CGD B:HEM501 3.3 71.2 1.0
CG2 B:VAL336 3.5 23.1 1.0
C15 B:V80503 3.6 63.8 1.0
C13 B:V80503 3.6 71.4 1.0
C06 B:V80503 4.0 28.4 1.0
C14 B:V80503 4.1 71.7 1.0
C05 B:V80503 4.2 15.2 1.0
O1D B:HEM501 4.2 60.6 1.0
C3D B:HEM501 4.3 31.8 1.0
C4D B:HEM501 4.4 24.0 1.0
CAD B:HEM501 4.4 41.4 1.0
CHA B:HEM501 4.4 21.8 1.0
CG1 B:VAL336 4.4 13.5 1.0
O B:HOH750 4.5 44.0 1.0
CB B:VAL336 4.6 19.1 1.0
O2A B:HEM501 4.7 79.1 1.0
CBA B:HEM501 4.7 42.5 1.0
C2D B:HEM501 4.9 19.9 1.0
SD B:MET339 4.9 31.9 1.0
ND B:HEM501 5.0 24.1 1.0

Fluorine binding site 4 out of 8 in 8fgq

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

b:83.8
occ:1.00
 F12 B:V80503 0.0 83.8 1.0
C12 B:V80503 1.3 75.8 1.0
C13 B:V80503 2.3 71.4 1.0
C11 B:V80503 2.4 68.2 1.0
F11 B:V80503 2.8 76.8 1.0
CGD B:HEM501 3.0 71.2 1.0
O1D B:HEM501 3.1 60.6 1.0
O B:HOH766 3.2 50.9 1.0
O2D B:HEM501 3.2 81.1 1.0
C14 B:V80503 3.6 71.7 1.0
C16 B:V80503 3.6 49.4 1.0
CBD B:HEM501 3.7 54.6 1.0
CE1 B:TYR475 4.0 31.2 1.0
O B:HOH750 4.0 44.0 1.0
C15 B:V80503 4.1 63.8 1.0
OH B:TYR475 4.2 59.5 1.0
CZ B:TYR475 4.6 44.3 1.0
O2A B:HEM501 4.7 79.1 1.0
C17 B:V80503 4.9 76.3 1.0
C09 B:V80503 4.9 32.9 1.0

Fluorine binding site 5 out of 8 in 8fgq

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

b:89.3
occ:1.00
 F11 C:V80503 0.0 89.3 1.0
C11 C:V80503 1.3 89.0 1.0
C12 C:V80503 2.3 91.7 1.0
C16 C:V80503 2.4 83.7 1.0
F12 C:V80503 2.6 93.1 1.0
C09 C:V80503 2.9 72.7 1.0
C08 C:V80503 3.0 61.3 1.0
CBD C:HEM501 3.2 62.3 1.0
CG2 C:VAL336 3.2 30.4 1.0
CGD C:HEM501 3.5 77.0 1.0
C13 C:V80503 3.6 90.4 1.0
C15 C:V80503 3.6 88.2 1.0
O2D C:HEM501 3.7 77.5 1.0
CG1 C:VAL336 4.0 24.9 1.0
C06 C:V80503 4.1 52.8 1.0
C14 C:V80503 4.1 90.2 1.0
CB C:VAL336 4.2 39.3 1.0
C05 C:V80503 4.2 49.1 1.0
O1D C:HEM501 4.3 86.1 1.0
CAD C:HEM501 4.5 44.3 1.0
C3D C:HEM501 4.6 40.8 1.0
C4D C:HEM501 4.7 42.1 1.0
CHA C:HEM501 4.7 40.6 1.0
SD C:MET339 4.8 45.0 1.0
O C:HOH672 4.9 56.5 1.0

Fluorine binding site 6 out of 8 in 8fgq

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

b:93.1
occ:1.00
 F12 C:V80503 0.0 93.1 1.0
C12 C:V80503 1.3 91.7 1.0
O2D C:HEM501 2.2 77.5 1.0
C11 C:V80503 2.4 89.0 1.0
C13 C:V80503 2.4 90.4 1.0
F11 C:V80503 2.6 89.3 1.0
CGD C:HEM501 3.1 77.0 1.0
CBD C:HEM501 3.6 62.3 1.0
C14 C:V80503 3.6 90.2 1.0
C16 C:V80503 3.6 83.7 1.0
O C:HOH726 3.7 38.9 1.0
CE1 C:TYR475 3.9 47.1 1.0
O1D C:HEM501 4.0 86.1 1.0
C15 C:V80503 4.1 88.2 1.0
OH C:TYR475 4.4 58.2 1.0
SD C:MET339 4.6 45.0 1.0
CZ C:TYR475 4.6 55.8 1.0
O C:HOH672 4.7 56.5 1.0
CD1 C:TYR475 4.8 44.3 1.0
C17 C:V80503 4.9 93.5 1.0
C09 C:V80503 4.9 72.7 1.0
CG1 C:VAL336 4.9 24.9 1.0

Fluorine binding site 7 out of 8 in 8fgq

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

b:73.6
occ:1.00
 F11 D:V80503 0.0 73.6 1.0
C11 D:V80503 1.3 70.9 1.0
C12 D:V80503 2.3 82.2 1.0
C16 D:V80503 2.4 55.7 1.0
F12 D:V80503 2.7 85.8 1.0
C09 D:V80503 2.8 36.0 1.0
C08 D:V80503 3.0 28.5 1.0
CG2 D:VAL336 3.1 14.9 1.0
CBD D:HEM501 3.3 49.3 1.0
C13 D:V80503 3.6 80.3 1.0
C15 D:V80503 3.6 68.6 1.0
O2D D:HEM501 3.9 68.5 1.0
CGD D:HEM501 3.9 65.4 1.0
C06 D:V80503 3.9 32.4 1.0
C05 D:V80503 4.0 24.7 1.0
C14 D:V80503 4.1 75.8 1.0
CG1 D:VAL336 4.2 13.6 1.0
CB D:VAL336 4.2 21.8 1.0
O D:HOH661 4.3 28.0 1.0
C4D D:HEM501 4.4 23.1 1.0
C3D D:HEM501 4.4 30.3 1.0
CHA D:HEM501 4.5 16.8 1.0
CAD D:HEM501 4.6 32.1 1.0
O D:HOH722 4.6 46.6 1.0
CBA D:HEM501 4.8 49.6 1.0
O1D D:HEM501 4.9 76.5 1.0
C2D D:HEM501 5.0 25.7 1.0
SD D:MET339 5.0 28.7 1.0
ND D:HEM501 5.0 19.3 1.0

Fluorine binding site 8 out of 8 in 8fgq

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

b:85.8
occ:1.00
 F12 D:V80503 0.0 85.8 1.0
C12 D:V80503 1.4 82.2 1.0
O2D D:HEM501 2.2 68.5 1.0
C11 D:V80503 2.4 70.9 1.0
C13 D:V80503 2.4 80.3 1.0
F11 D:V80503 2.7 73.6 1.0
O D:HOH661 2.8 28.0 1.0
CGD D:HEM501 3.1 65.4 1.0
CBD D:HEM501 3.3 49.3 1.0
O D:HOH788 3.6 63.5 1.0
C16 D:V80503 3.6 55.7 1.0
C14 D:V80503 3.6 75.8 1.0
CE1 D:TYR475 3.8 35.3 1.0
C15 D:V80503 4.1 68.6 1.0
O1D D:HEM501 4.2 76.5 1.0
OH D:TYR475 4.3 51.2 1.0
O D:HOH722 4.3 46.6 1.0
SD D:MET339 4.5 28.7 1.0
CZ D:TYR475 4.6 42.5 1.0
CAD D:HEM501 4.8 32.1 1.0
CD1 D:TYR475 4.8 28.8 1.0
C17 D:V80503 4.9 79.5 1.0
C09 D:V80503 4.9 36.0 1.0
CG1 D:VAL336 4.9 13.6 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 18:53:28 2024

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