Gadolinium in PDB 6nh8: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(3-(Dimethylamino)Propyl)-2,3,4- Trifluorophenethyl)-4-Methylpyridin-2-Amine

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(3-(Dimethylamino)Propyl)-2,3,4- Trifluorophenethyl)-4-Methylpyridin-2-Amine, PDB code: 6nh8 was solved by G.Chreifi, H.Li, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.61 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.720, 152.510, 108.530, 90.00, 90.70, 90.00
R / Rfree (%)	20 / 23.4

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

Fluorine	(F)	12 atoms
Zinc	(Zn)	2 atoms
Iron	(Fe)	4 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Gadolinium atom in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(3-(Dimethylamino)Propyl)-2,3,4- Trifluorophenethyl)-4-Methylpyridin-2-Amine (pdb code 6nh8). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 4 binding sites of Gadolinium where determined in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(3-(Dimethylamino)Propyl)-2,3,4- Trifluorophenethyl)-4-Methylpyridin-2-Amine, PDB code: 6nh8:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(3-(Dimethylamino)Propyl)-2,3,4- Trifluorophenethyl)-4-Methylpyridin-2-Amine


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(3-(Dimethylamino)Propyl)-2,3,4- Trifluorophenethyl)-4-Methylpyridin-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd510 b:90.4 occ:1.00 O A:HOH645 2.7 49.1 1.0 O4 A:BTB504 2.7 78.2 1.0 O3 A:BTB504 2.7 47.4 1.0 N A:BTB504 2.7 73.8 1.0 O6 A:BTB504 2.8 79.9 1.0 O A:HOH736 2.8 54.8 1.0 O8 A:BTB504 2.8 76.2 1.0 C7 A:BTB504 3.3 72.3 1.0 C2 A:BTB504 3.4 66.7 1.0 C8 A:BTB504 3.6 73.9 1.0 C3 A:BTB504 3.6 58.0 1.0 C4 A:BTB504 3.6 73.2 1.0 C6 A:BTB504 3.7 78.0 1.0 C5 A:BTB504 3.7 77.0 1.0 OD1 A:ASP384 4.6 65.8 1.0 OD2 A:ASP384 4.6 65.7 1.0 C1 A:BTB504 4.8 67.0 1.0

Gadolinium binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(3-(Dimethylamino)Propyl)-2,3,4- Trifluorophenethyl)-4-Methylpyridin-2-Amine


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(3-(Dimethylamino)Propyl)-2,3,4- Trifluorophenethyl)-4-Methylpyridin-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:Gd508 b:34.7 occ:1.00 O B:THR319 2.4 27.9 1.0 O3 B:BTB504 2.6 33.6 1.0 O4 B:BTB504 2.7 53.3 1.0 O B:HOH736 2.7 52.9 1.0 N B:BTB504 2.7 51.8 1.0 O6 B:BTB504 2.7 41.9 1.0 OE1 B:GLU321 2.7 47.8 1.0 O8 B:BTB504 2.7 47.8 1.0 O C:HOH607 2.8 36.9 1.0 C6 B:BTB504 2.8 30.9 1.0 C8 B:BTB504 3.1 46.8 1.0 C5 B:BTB504 3.4 50.9 1.0 C2 B:BTB504 3.4 58.8 1.0 C7 B:BTB504 3.5 47.3 1.0 C3 B:BTB504 3.5 46.9 1.0 C4 B:BTB504 3.6 57.2 1.0 C B:THR319 3.6 43.6 1.0 CD B:GLU321 3.8 47.1 1.0 OE2 B:GLU321 4.1 49.9 1.0 CA B:THR319 4.4 30.2 1.0 O B:HOH795 4.4 47.7 1.0 N B:LEU320 4.5 33.4 1.0 N B:GLU321 4.5 28.9 1.0 OD1 C:ASP378 4.6 41.9 1.0 CA B:LEU320 4.6 28.8 1.0 OD2 C:ASP378 4.6 46.9 1.0 CB B:THR319 4.6 38.5 1.0 O B:HOH668 4.7 41.5 1.0 C1 B:BTB504 4.9 66.5 1.0

Gadolinium binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(3-(Dimethylamino)Propyl)-2,3,4- Trifluorophenethyl)-4-Methylpyridin-2-Amine


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(3-(Dimethylamino)Propyl)-2,3,4- Trifluorophenethyl)-4-Methylpyridin-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ C:Gd510 b:81.0 occ:1.00 O3 C:BTB504 2.4 12.5 1.0 O C:HOH601 2.7 33.5 1.0 O4 C:BTB504 2.7 68.8 1.0 O C:HOH741 2.8 46.9 1.0 N C:BTB504 2.9 57.7 1.0 O8 C:BTB504 3.0 48.3 1.0 O6 C:BTB504 3.1 58.0 1.0 O C:HOH767 3.3 53.8 1.0 C3 C:BTB504 3.4 40.2 1.0 C8 C:BTB504 3.4 55.3 1.0 C2 C:BTB504 3.4 56.2 1.0 C6 C:BTB504 3.5 54.8 1.0 C4 C:BTB504 3.5 64.6 1.0 C7 C:BTB504 3.8 59.4 1.0 C5 C:BTB504 3.8 55.2 1.0 O C:HOH602 3.9 63.9 1.0 OD2 C:ASP384 4.5 57.8 1.0 OD1 C:ASP384 4.7 71.3 1.0 C1 C:BTB504 4.9 61.0 1.0

Gadolinium binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(3-(Dimethylamino)Propyl)-2,3,4- Trifluorophenethyl)-4-Methylpyridin-2-Amine


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(3-(Dimethylamino)Propyl)-2,3,4- Trifluorophenethyl)-4-Methylpyridin-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ D:Gd507 b:36.4 occ:1.00 O D:THR319 2.4 28.8 1.0 O D:HOH783 2.5 40.1 1.0 O4 D:BTB504 2.6 58.7 1.0 C6 D:BTB504 2.7 37.2 1.0 N D:BTB504 2.7 68.1 1.0 O6 D:BTB504 2.7 43.7 1.0 O3 D:BTB504 2.7 58.4 1.0 OE1 D:GLU321 2.7 60.7 1.0 O8 D:BTB504 2.8 55.9 1.0 C5 D:BTB504 3.2 46.2 1.0 C4 D:BTB504 3.3 60.0 1.0 C2 D:BTB504 3.3 72.2 1.0 C3 D:BTB504 3.5 66.8 1.0 C D:THR319 3.6 48.8 1.0 C8 D:BTB504 3.6 61.5 1.0 CD D:GLU321 3.7 55.6 1.0 C7 D:BTB504 3.7 66.0 1.0 OE2 D:GLU321 3.9 69.7 1.0 O D:HOH834 4.2 49.6 1.0 O D:HOH656 4.2 43.8 1.0 CA D:THR319 4.4 27.7 1.0 N D:LEU320 4.5 34.0 1.0 N D:GLU321 4.6 36.2 1.0 CA D:LEU320 4.6 32.8 1.0 CB D:THR319 4.6 41.3 1.0 C1 D:BTB504 4.8 78.8 1.0

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