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Iron 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
Fluorine (F) 8 atoms
Chlorine (Cl) 4 atoms
Gadolinium (Gd) 4 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron 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 Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8fgt

Go back to Iron Binding Sites List in 8fgt
Iron binding site 1 out of 4 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 Iron with other atoms in the Fe 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:Fe501

b:40.8
occ:1.00
 FE A:HEM501 0.0 40.8 1.0
ND A:HEM501 2.0 40.9 1.0
NA A:HEM501 2.1 45.5 1.0
NB A:HEM501 2.1 45.3 1.0
NC A:HEM501 2.1 40.5 1.0
SG A:CYS184 2.2 42.3 1.0
C4D A:HEM501 3.0 46.2 1.0
C1A A:HEM501 3.0 45.6 1.0
C4B A:HEM501 3.1 51.7 1.0
C1C A:HEM501 3.1 47.6 1.0
C1D A:HEM501 3.1 49.7 1.0
C4A A:HEM501 3.1 51.5 1.0
C1B A:HEM501 3.1 56.3 1.0
C4C A:HEM501 3.1 49.9 1.0
CHA A:HEM501 3.3 41.5 1.0
CHC A:HEM501 3.4 45.6 1.0
CB A:CYS184 3.5 41.7 1.0
CHB A:HEM501 3.5 54.4 1.0
CHD A:HEM501 3.5 48.7 1.0
C03 A:XVK504 4.0 63.8 1.0
C04 A:XVK504 4.1 66.7 1.0
CA A:CYS184 4.1 43.1 1.0
NE1 A:TRP178 4.2 46.8 1.0
C3D A:HEM501 4.2 58.3 1.0
C2D A:HEM501 4.3 53.6 1.0
C2A A:HEM501 4.3 45.8 1.0
C2B A:HEM501 4.3 51.7 1.0
C3B A:HEM501 4.3 51.9 1.0
C3A A:HEM501 4.3 50.7 1.0
C2C A:HEM501 4.3 52.5 1.0
C3C A:HEM501 4.3 53.5 1.0
C07 A:XVK504 4.4 65.1 1.0
C02 A:XVK504 4.4 56.9 1.0
C05 A:XVK504 4.7 75.6 1.0
CD1 A:TRP178 4.8 50.0 1.0
N02 A:XVK504 4.9 48.9 1.0
F12 A:XVK504 4.9 126.8 1.0
C A:CYS184 4.9 43.3 1.0
N01 A:XVK504 5.0 62.8 1.0

Iron binding site 2 out of 4 in 8fgt

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Iron binding site 2 out of 4 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 Iron with other atoms in the Fe 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
B:Fe501

b:32.1
occ:1.00
 FE B:HEM501 0.0 32.1 1.0
ND B:HEM501 2.0 33.8 1.0
NA B:HEM501 2.0 36.8 1.0
NB B:HEM501 2.1 34.6 1.0
NC B:HEM501 2.1 26.0 1.0
SG B:CYS184 2.4 29.5 1.0
C4D B:HEM501 3.0 33.9 1.0
C4A B:HEM501 3.0 29.2 1.0
C1D B:HEM501 3.1 35.9 1.0
C1A B:HEM501 3.1 31.4 1.0
C1B B:HEM501 3.1 26.8 1.0
C1C B:HEM501 3.1 29.0 1.0
C4B B:HEM501 3.1 36.1 1.0
C4C B:HEM501 3.1 29.5 1.0
CB B:CYS184 3.3 23.6 1.0
CHB B:HEM501 3.4 28.2 1.0
CHA B:HEM501 3.4 24.4 1.0
CHD B:HEM501 3.4 27.7 1.0
CHC B:HEM501 3.5 31.1 1.0
CA B:CYS184 4.0 23.6 1.0
C03 B:XVK503 4.1 30.3 1.0
NE1 B:TRP178 4.2 34.9 1.0
C3D B:HEM501 4.2 30.8 1.0
C2D B:HEM501 4.2 35.4 1.0
C2B B:HEM501 4.3 31.9 1.0
C3A B:HEM501 4.3 29.4 1.0
C2A B:HEM501 4.3 29.5 1.0
C3B B:HEM501 4.3 32.5 1.0
C2C B:HEM501 4.4 25.1 1.0
C3C B:HEM501 4.4 34.0 1.0
C04 B:XVK503 4.4 40.1 1.0
F12 B:XVK503 4.4 110.7 1.0
C02 B:XVK503 4.6 33.9 1.0
C07 B:XVK503 4.6 29.2 1.0
N B:GLY186 4.7 34.0 1.0
C B:CYS184 4.8 28.7 1.0
CD1 B:TRP178 4.9 31.2 1.0
N B:VAL185 4.9 27.1 1.0
N02 B:XVK503 5.0 31.2 1.0

Iron binding site 3 out of 4 in 8fgt

Go back to Iron Binding Sites List in 8fgt
Iron binding site 3 out of 4 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 Iron with other atoms in the Fe 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
C:Fe501

b:39.0
occ:1.00
 FE C:HEM501 0.0 39.0 1.0
NC C:HEM501 2.1 45.9 1.0
ND C:HEM501 2.1 37.9 1.0
NB C:HEM501 2.1 40.3 1.0
NA C:HEM501 2.1 41.0 1.0
SG C:CYS184 2.3 38.1 1.0
C4B C:HEM501 3.0 42.8 1.0
C1C C:HEM501 3.0 49.7 1.0
C4D C:HEM501 3.1 43.5 1.0
C1A C:HEM501 3.1 42.8 1.0
C1B C:HEM501 3.1 41.3 1.0
C1D C:HEM501 3.1 45.4 1.0
C4C C:HEM501 3.1 48.1 1.0
C4A C:HEM501 3.1 45.9 1.0
CB C:CYS184 3.3 34.0 1.0
CHC C:HEM501 3.4 45.2 1.0
CHA C:HEM501 3.4 31.4 1.0
CHD C:HEM501 3.5 46.3 1.0
CHB C:HEM501 3.5 34.0 1.0
CA C:CYS184 4.1 40.0 1.0
C03 C:XVK503 4.1 49.1 1.0
C3B C:HEM501 4.3 38.8 1.0
NE1 C:TRP178 4.3 44.2 1.0
C2B C:HEM501 4.3 37.4 1.0
C2C C:HEM501 4.3 53.0 1.0
C3D C:HEM501 4.3 44.2 1.0
C2D C:HEM501 4.3 35.5 1.0
C2A C:HEM501 4.3 47.9 1.0
C3C C:HEM501 4.3 46.2 1.0
C3A C:HEM501 4.3 41.7 1.0
C04 C:XVK503 4.4 55.4 1.0
C02 C:XVK503 4.6 47.9 1.0
C07 C:XVK503 4.6 62.9 1.0
N C:GLY186 4.7 43.8 1.0
C C:CYS184 4.7 34.9 1.0
N C:VAL185 4.9 38.9 1.0
CD1 C:TRP178 4.9 51.1 1.0
N02 C:XVK503 4.9 40.0 1.0

Iron binding site 4 out of 4 in 8fgt

Go back to Iron Binding Sites List in 8fgt
Iron binding site 4 out of 4 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 Iron with other atoms in the Fe 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
D:Fe501

b:31.6
occ:1.00
 FE D:HEM501 0.0 31.6 1.0
ND D:HEM501 2.0 32.6 1.0
NA D:HEM501 2.0 24.1 1.0
NB D:HEM501 2.1 29.8 1.0
NC D:HEM501 2.1 28.0 1.0
SG D:CYS184 2.3 31.5 1.0
C4D D:HEM501 3.0 34.4 1.0
C1A D:HEM501 3.0 29.8 1.0
C1D D:HEM501 3.0 33.7 1.0
C4A D:HEM501 3.1 26.0 1.0
C4C D:HEM501 3.1 33.3 1.0
C1B D:HEM501 3.1 32.6 1.0
C1C D:HEM501 3.2 29.9 1.0
C4B D:HEM501 3.2 26.5 1.0
CB D:CYS184 3.3 28.8 1.0
CHA D:HEM501 3.3 28.9 1.0
CHD D:HEM501 3.4 26.2 1.0
CHB D:HEM501 3.4 33.0 1.0
CHC D:HEM501 3.6 31.2 1.0
CA D:CYS184 4.0 21.3 1.0
C03 D:XVK503 4.1 29.6 1.0
C3D D:HEM501 4.2 35.5 1.0
C2D D:HEM501 4.2 33.9 1.0
C2A D:HEM501 4.2 34.3 1.0
C3A D:HEM501 4.3 26.1 1.0
C2B D:HEM501 4.3 31.5 1.0
C3C D:HEM501 4.3 30.6 1.0
NE1 D:TRP178 4.3 31.2 1.0
C2C D:HEM501 4.4 29.8 1.0
C3B D:HEM501 4.4 28.9 1.0
C04 D:XVK503 4.4 38.9 1.0
F12 D:XVK503 4.6 99.4 1.0
C07 D:XVK503 4.6 26.5 1.0
C02 D:XVK503 4.6 34.0 1.0
N D:GLY186 4.7 28.4 1.0
C D:CYS184 4.8 31.6 1.0
N D:VAL185 4.9 32.2 1.0
CD1 D:TRP178 4.9 31.8 1.0
CA D:GLY186 5.0 27.8 1.0
N02 D:XVK503 5.0 28.9 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: Sat Aug 10 03:53:57 2024

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