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

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 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 Zinc with other atoms in the Zn 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:Zn505 b:42.1 occ:1.00 SG A:CYS99 2.3 38.8 1.0 SG A:CYS94 2.3 43.2 1.0 SG B:CYS99 2.4 38.8 1.0 SG B:CYS94 2.4 37.7 1.0 CB B:CYS99 3.2 34.4 1.0 CB A:CYS99 3.3 33.0 1.0 CB A:CYS94 3.3 43.1 1.0 CB B:CYS94 3.4 42.1 1.0 CA B:CYS99 3.6 35.9 1.0 CA A:CYS99 3.7 40.6 1.0 N B:GLY101 4.1 35.1 1.0 N B:LEU100 4.1 32.9 1.0 N A:LEU100 4.2 49.8 1.0 N A:GLY101 4.2 44.5 1.0 C B:CYS99 4.3 41.1 1.0 C A:CYS99 4.3 46.5 1.0 CA B:GLY101 4.5 37.9 1.0 CA A:GLY101 4.5 46.1 1.0 CA A:CYS94 4.7 47.3 1.0 CA B:CYS94 4.8 49.4 1.0 N B:CYS99 4.9 34.7 1.0 C A:LEU100 5.0 44.9 1.0 N A:CYS99 5.0 34.8 1.0

Zinc binding site 2 out of 6 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 Zinc with other atoms in the Zn 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 A:Zn508 b:42.8 occ:0.68 OD2 A:ASP369 2.0 45.8 1.0 O A:HOH677 2.0 30.2 1.0 O A:HOH673 2.1 28.1 1.0 NE2 B:HIS461 2.2 44.3 1.0 OD1 A:ASP369 2.3 42.4 1.0 CG A:ASP369 2.5 42.4 1.0 CD2 B:HIS461 3.1 41.6 1.0 CE1 B:HIS461 3.3 41.2 1.0 CG A:ARG365 3.9 52.9 1.0 CB A:ASP369 4.0 42.2 1.0 O A:HOH654 4.2 42.3 1.0 CB A:ARG365 4.3 37.2 1.0 CG B:HIS461 4.3 36.0 1.0 ND1 B:HIS461 4.3 37.3 1.0 CD A:ARG365 4.4 61.9 1.0 CE1 A:HIS371 4.4 45.9 1.0 CE2 B:PHE460 4.4 40.4 1.0 CA A:ARG365 4.5 33.3 1.0 O A:HOH631 4.5 39.2 1.0 CB B:SER455 4.6 37.6 1.0 CD2 B:PHE460 4.6 34.2 1.0 O A:HOH686 4.6 34.8 1.0 NE2 A:HIS371 4.9 49.3 1.0 CA A:ASP369 5.0 39.5 1.0

Zinc binding site 3 out of 6 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 Zinc with other atoms in the Zn 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 A:Zn510 b:37.3 occ:0.79 OD2 B:ASP369 2.0 32.4 1.0 NE2 A:HIS461 2.2 44.6 1.0 O B:HOH1040 2.2 22.0 1.0 OD1 B:ASP369 2.3 35.7 1.0 O B:HOH1042 2.4 22.6 1.0 CG B:ASP369 2.5 35.3 1.0 CD2 A:HIS461 3.1 45.2 1.0 CE1 A:HIS461 3.2 40.1 1.0 O B:HOH923 3.8 35.2 1.0 CG B:ARG365 4.0 34.7 1.0 CB B:ASP369 4.0 30.1 1.0 ND1 A:HIS461 4.3 41.5 1.0 CG A:HIS461 4.3 40.3 1.0 CE1 B:HIS371 4.3 41.2 1.0 CE2 A:PHE460 4.3 32.6 1.0 CB B:ARG365 4.4 29.8 1.0 CA B:ARG365 4.4 25.9 1.0 O B:HOH1044 4.5 41.5 1.0 CD B:ARG365 4.6 34.6 1.0 O B:HOH984 4.6 36.0 1.0 CD2 A:PHE460 4.6 31.3 1.0 CB A:SER455 4.6 30.2 1.0 NE2 B:HIS371 4.7 41.3 1.0 O B:ARG365 5.0 28.3 1.0 CA B:ASP369 5.0 31.6 1.0

Zinc binding site 4 out of 6 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 Zinc with other atoms in the Zn 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 C:Zn506 b:36.0 occ:1.00 SG C:CYS94 2.2 34.2 1.0 SG C:CYS99 2.4 40.5 1.0 SG D:CYS99 2.5 33.8 1.0 SG D:CYS94 2.5 33.3 1.0 CB C:CYS99 2.5 42.0 1.0 CB D:CYS99 3.2 30.1 1.0 CB C:CYS94 3.3 35.0 1.0 CB D:CYS94 3.3 30.4 1.0 CA C:CYS99 3.5 43.1 1.0 CA D:CYS99 3.7 37.2 1.0 N C:GLY101 4.0 37.3 1.0 C C:CYS99 4.1 44.6 1.0 N D:GLY101 4.1 38.1 1.0 N C:LEU100 4.1 45.8 1.0 N D:LEU100 4.2 36.5 1.0 C D:CYS99 4.3 41.9 1.0 CA C:GLY101 4.3 40.3 1.0 CA D:GLY101 4.4 34.8 1.0 CA C:CYS94 4.6 38.9 1.0 N C:CYS99 4.7 31.8 1.0 CA D:CYS94 4.8 41.3 1.0 C C:LEU100 4.9 35.3 1.0 N D:CYS99 5.0 37.2 1.0

Zinc binding site 5 out of 6 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 Zinc with other atoms in the Zn binding site number 5 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:Zn510 b:35.7 occ:0.57 O C:HOH694 2.0 25.0 1.0 OD2 C:ASP369 2.1 43.5 1.0 NE2 D:HIS461 2.2 37.5 1.0 O C:HOH692 2.2 25.4 1.0 OD1 C:ASP369 2.3 36.8 1.0 CG C:ASP369 2.6 42.2 1.0 CD2 D:HIS461 3.1 38.4 1.0 CE1 D:HIS461 3.2 32.1 1.0 CG C:ARG365 3.8 55.3 1.0 O C:HOH633 3.9 40.0 1.0 CB C:ASP369 4.1 40.7 1.0 CG D:HIS461 4.3 35.2 1.0 CE2 D:PHE460 4.3 29.7 1.0 ND1 D:HIS461 4.3 39.6 1.0 CB C:ARG365 4.3 32.7 1.0 CE1 C:HIS371 4.4 42.4 1.0 CD C:ARG365 4.4 66.5 1.0 CA C:ARG365 4.5 32.6 1.0 CD2 D:PHE460 4.5 26.4 1.0 NE2 C:HIS371 4.6 41.1 1.0 O C:HOH641 4.6 34.7 1.0 CB D:SER455 4.6 35.9 1.0

Zinc binding site 6 out of 6 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 Zinc with other atoms in the Zn binding site number 6 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:Zn512 b:41.9 occ:0.87 OD2 D:ASP369 2.0 35.1 1.0 NE2 C:HIS461 2.1 47.2 1.0 O D:HOH754 2.2 23.6 1.0 OD1 D:ASP369 2.3 40.9 1.0 O D:HOH762 2.4 24.6 1.0 CG D:ASP369 2.5 31.7 1.0 CE1 C:HIS461 3.0 44.5 1.0 CD2 C:HIS461 3.2 47.1 1.0 CG D:ARG365 4.0 38.2 1.0 CB D:ASP369 4.0 28.4 1.0 O D:HOH703 4.1 46.2 1.0 ND1 C:HIS461 4.2 45.4 1.0 CE1 D:HIS371 4.3 49.3 1.0 CE1 C:PHE460 4.3 24.8 1.0 CG C:HIS461 4.3 43.6 1.0 O D:HOH722 4.4 51.2 1.0 CB D:ARG365 4.5 31.4 1.0 CA D:ARG365 4.5 32.4 1.0 O C:HOH699 4.5 53.9 1.0 CD1 C:PHE460 4.6 24.7 1.0 NE2 D:HIS371 4.6 49.1 1.0 O D:HOH773 4.6 33.6 1.0 CD D:ARG365 4.6 37.6 1.0 CB C:SER455 4.6 41.1 1.0 O D:HOH712 4.7 33.3 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