Gadolinium in PDB 6nh3: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine, PDB code: 6nh3 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)	88.87 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.469, 153.089, 109.150, 90.00, 90.80, 90.00
R / Rfree (%)	20.6 / 25.7

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

Fluorine	(F)	8 atoms
Zinc	(Zn)	6 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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine (pdb code 6nh3). 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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine, PDB code: 6nh3:
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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd511 b:87.4 occ:1.00 OD1 A:ASP384 2.7 85.3 1.0 O C:HOH711 2.7 71.0 1.0 OE1 C:GLN257 2.8 0.9 1.0 O A:HOH687 2.8 34.1 1.0 O A:HOH670 2.9 0.9 1.0 CD C:GLN257 3.3 0.5 1.0 O C:HOH719 3.7 65.8 1.0 O C:GLN257 3.7 0.2 1.0 CG A:ASP384 3.8 81.3 1.0 O A:HOH693 3.8 45.8 1.0 CG C:GLN257 3.9 0.8 1.0 CB C:GLN257 3.9 0.0 1.0 NE2 C:GLN257 4.1 0.4 1.0 O A:LEU385 4.3 43.4 1.0 OD2 A:ASP384 4.4 84.9 1.0 C C:GLN257 4.6 0.0 1.0 O A:ASP384 4.7 46.3 1.0 C A:ASP384 4.8 49.1 1.0 CA C:GLN257 4.8 0.5 1.0 CA A:ASP384 4.8 47.4 1.0 CB A:ASP384 4.9 61.2 1.0

Gadolinium binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:Gd807 b:48.2 occ:1.00 O3 B:BTB804 2.5 49.0 1.0 O C:HOH608 2.6 43.8 1.0 O B:THR319 2.6 54.7 1.0 O4 B:BTB804 2.6 57.9 1.0 OE1 B:GLU321 2.7 60.5 1.0 O8 B:BTB804 2.7 46.1 1.0 C6 B:BTB804 2.8 27.9 1.0 N B:BTB804 2.8 44.1 1.0 O6 B:BTB804 2.8 42.8 1.0 C5 B:BTB804 3.3 28.2 1.0 C3 B:BTB804 3.4 68.0 1.0 C2 B:BTB804 3.4 67.2 1.0 C8 B:BTB804 3.5 45.3 1.0 C4 B:BTB804 3.6 68.8 1.0 C7 B:BTB804 3.7 42.0 1.0 CD B:GLU321 3.7 54.1 1.0 C B:THR319 3.7 56.8 1.0 OE2 B:GLU321 4.0 55.8 1.0 CA B:THR319 4.5 47.9 1.0 OD1 C:ASP378 4.5 65.0 1.0 N B:GLU321 4.6 46.5 1.0 N B:LEU320 4.6 59.2 1.0 CB B:THR319 4.6 43.9 1.0 CA B:LEU320 4.6 45.0 1.0 OD2 C:ASP378 4.8 63.2 1.0 C1 B:BTB804 4.9 74.9 1.0

Gadolinium binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ C:Gd509 b:1.0 occ:1.00 O4 C:BTB504 2.7 88.4 1.0 N C:BTB504 3.2 0.3 1.0 C8 C:BTB504 3.3 0.9 1.0 C7 C:BTB504 3.5 0.5 1.0 O8 C:BTB504 3.6 0.2 1.0 C4 C:BTB504 3.9 97.4 1.0 O6 C:BTB504 3.9 1.0 1.0 C6 C:BTB504 4.0 0.1 1.0 O3 C:BTB504 4.0 85.5 1.0 C2 C:BTB504 4.1 0.3 1.0 C5 C:BTB504 4.2 0.4 1.0 OD2 C:ASP384 4.2 79.8 1.0 OD1 C:ASP384 4.4 84.8 1.0 C3 C:BTB504 4.7 91.1 1.0 CG C:ASP384 4.7 76.1 1.0

Gadolinium binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ D:Gd505 b:48.5 occ:1.00 O D:HOH607 2.5 26.6 1.0 O D:THR319 2.6 23.6 1.0 O3 D:BTB503 2.6 54.2 1.0 O D:HOH705 2.6 49.5 1.0 O4 D:BTB503 2.6 57.5 1.0 OE1 D:GLU321 2.7 72.3 1.0 N D:BTB503 2.7 71.6 1.0 O8 D:BTB503 2.7 68.0 1.0 O6 D:BTB503 2.8 56.8 1.0 OE2 D:GLU321 2.8 65.8 1.0 C6 D:BTB503 2.9 45.0 1.0 C5 D:BTB503 3.1 51.6 1.0 CD D:GLU321 3.1 62.0 1.0 C2 D:BTB503 3.4 73.9 1.0 C3 D:BTB503 3.4 65.9 1.0 C4 D:BTB503 3.6 69.2 1.0 C8 D:BTB503 3.6 71.4 1.0 C7 D:BTB503 3.7 71.4 1.0 C D:THR319 3.7 44.0 1.0 O D:HOH682 4.4 50.9 1.0 CA D:THR319 4.5 45.0 1.0 CB D:THR319 4.6 39.7 1.0 CA D:LEU320 4.6 42.5 1.0 CG D:GLU321 4.6 48.7 1.0 N D:GLU321 4.7 43.7 1.0 N D:LEU320 4.7 43.2 1.0 C1 D:BTB503 4.9 78.3 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