Gadolinium in PDB 6nh4: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoropyrrolidin-2-Yl) Ethyl)Phenethyl)-4-Methylpyridin-2-Amine

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoropyrrolidin-2-Yl) Ethyl)Phenethyl)-4-Methylpyridin-2-Amine, PDB code: 6nh4 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)	39.98 / 2.27
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.708, 152.546, 109.139, 90.00, 90.87, 90.00
R / Rfree (%)	19.2 / 25.1

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

Fluorine	(F)	12 atoms
Zinc	(Zn)	6 atoms
Iron	(Fe)	4 atoms
Chlorine	(Cl)	7 atoms

The binding sites of Gadolinium atom in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoropyrrolidin-2-Yl) Ethyl)Phenethyl)-4-Methylpyridin-2-Amine (pdb code 6nh4). 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-(3-Fluoro-5-(2-((2R,4S)-4-Fluoropyrrolidin-2-Yl) Ethyl)Phenethyl)-4-Methylpyridin-2-Amine, PDB code: 6nh4:
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-(3-Fluoro-5-(2-((2R,4S)-4-Fluoropyrrolidin-2-Yl) Ethyl)Phenethyl)-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-(3-Fluoro-5-(2-((2R,4S)-4-Fluoropyrrolidin-2-Yl) Ethyl)Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:Gd507 b:34.9 occ:1.00 O B:HOH722 2.6 35.3 1.0 N B:BTB504 2.6 47.4 1.0 O4 B:BTB504 2.7 54.2 1.0 O B:THR319 2.7 52.6 1.0 O3 B:BTB504 2.7 33.0 1.0 O8 B:BTB504 2.7 48.4 1.0 O6 B:BTB504 2.7 43.0 1.0 OE1 B:GLU321 2.8 49.0 1.0 C8 B:BTB504 3.0 46.5 1.0 C6 B:BTB504 3.1 44.2 1.0 C2 B:BTB504 3.3 56.0 1.0 C7 B:BTB504 3.4 43.6 1.0 C5 B:BTB504 3.5 41.1 1.0 C3 B:BTB504 3.5 50.4 1.0 C4 B:BTB504 3.5 59.3 1.0 C B:THR319 3.6 36.7 1.0 CD B:GLU321 3.9 47.2 1.0 OD1 C:ASP378 4.3 48.4 1.0 CA B:THR319 4.3 34.3 1.0 O B:HOH719 4.3 33.4 1.0 OE2 B:GLU321 4.4 49.1 1.0 N B:LEU320 4.5 40.2 1.0 CA B:LEU320 4.6 38.5 1.0 OD2 C:ASP378 4.6 42.8 1.0 N B:GLU321 4.6 30.1 1.0 CB B:THR319 4.7 32.7 1.0 O B:HOH662 4.8 38.5 1.0 C1 B:BTB504 4.8 56.1 1.0 CG C:ASP378 4.9 43.3 1.0

Gadolinium binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoropyrrolidin-2-Yl) Ethyl)Phenethyl)-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-(3-Fluoro-5-(2-((2R,4S)-4-Fluoropyrrolidin-2-Yl) Ethyl)Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ C:Gd501 b:0.9 occ:1.00 NE2 C:GLN257 2.5 95.9 1.0 O3 A:BTB503 2.6 86.0 1.0 O6 A:BTB503 2.6 92.8 1.0 OD1 A:ASP384 2.7 78.7 1.0 O4 A:BTB503 2.7 88.6 1.0 OE1 C:GLN257 2.8 0.1 1.0 O8 A:BTB503 2.8 69.4 1.0 CD C:GLN257 3.0 94.5 1.0 N A:BTB503 3.1 85.9 1.0 O A:HOH684 3.4 25.1 1.0 C6 A:BTB503 3.4 88.0 1.0 O C:GLN257 3.7 55.5 1.0 C3 A:BTB503 3.7 72.3 1.0 C5 A:BTB503 3.7 88.6 1.0 C2 A:BTB503 3.8 79.0 1.0 C8 A:BTB503 3.8 75.3 1.0 C4 A:BTB503 3.8 84.6 1.0 CG A:ASP384 3.9 69.4 1.0 C7 A:BTB503 4.0 78.0 1.0 OD2 A:ASP384 4.3 80.3 1.0 O A:HOH623 4.4 32.1 1.0 CG C:GLN257 4.5 70.4 1.0 O A:ASP384 4.6 40.2 1.0 O A:LEU385 4.8 35.7 1.0 C C:GLN257 4.8 44.5 1.0 C A:ASP384 4.9 35.7 1.0

Gadolinium binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoropyrrolidin-2-Yl) Ethyl)Phenethyl)-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-(3-Fluoro-5-(2-((2R,4S)-4-Fluoropyrrolidin-2-Yl) Ethyl)Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ C:Gd512 b:1.0 occ:1.00 CL C:CL511 2.7 0.9 1.0 CL C:CL510 2.7 0.1 1.0 O C:HOH640 3.3 38.8 1.0 O B:HOH754 3.3 30.9 1.0 O B:HOH750 3.6 28.3 1.0 CL B:CL509 3.7 0.2 1.0 O C:LEU385 4.3 40.4 1.0 O C:ASP384 4.6 26.4 1.0 C C:ASP384 4.9 27.4 1.0

Gadolinium binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoropyrrolidin-2-Yl) Ethyl)Phenethyl)-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-(3-Fluoro-5-(2-((2R,4S)-4-Fluoropyrrolidin-2-Yl) Ethyl)Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ D:Gd506 b:43.1 occ:1.00 O4 D:BTB504 2.5 32.2 1.0 OE1 D:GLU321 2.6 42.8 1.0 O D:THR319 2.7 23.6 1.0 O3 D:BTB504 2.7 31.3 1.0 O D:HOH694 2.8 52.4 1.0 N D:BTB504 2.9 66.7 1.0 O8 D:BTB504 3.0 67.6 1.0 O6 D:BTB504 3.0 44.4 1.0 OE2 D:GLU321 3.1 54.1 1.0 CD D:GLU321 3.3 47.2 1.0 C3 D:BTB504 3.3 57.8 1.0 C6 D:BTB504 3.3 41.4 1.0 C5 D:BTB504 3.4 47.3 1.0 C2 D:BTB504 3.4 67.5 1.0 C4 D:BTB504 3.6 53.7 1.0 C D:THR319 3.7 37.8 1.0 C8 D:BTB504 3.8 69.9 1.0 C7 D:BTB504 3.8 69.4 1.0 CA D:THR319 4.4 35.7 1.0 CB D:THR319 4.6 39.3 1.0 N D:LEU320 4.7 43.7 1.0 O D:HOH709 4.7 47.5 1.0 CA D:LEU320 4.7 33.7 1.0 N D:GLU321 4.7 27.1 1.0 CG D:GLU321 4.8 38.2 1.0 C1 D:BTB504 4.9 71.7 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