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Gadolinium in PDB 6nh6: Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,6- Difluorophenethyl)-4-Methylpyridin-2-Amine

Protein crystallography data

The structure of Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,6- Difluorophenethyl)-4-Methylpyridin-2-Amine, PDB code: 6nh6 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) 76.41 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.860, 152.820, 109.190, 90.00, 91.00, 90.00
R / Rfree (%) 19.6 / 24.7

Other elements in 6nh6:

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

Fluorine (F) 8 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms
Chlorine (Cl) 4 atoms

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,6- Difluorophenethyl)-4-Methylpyridin-2-Amine (pdb code 6nh6). 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 the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,6- Difluorophenethyl)-4-Methylpyridin-2-Amine, PDB code: 6nh6:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 6nh6

Go back to Gadolinium Binding Sites List in 6nh6
Gadolinium binding site 1 out of 4 in the Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,6- Difluorophenethyl)-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 the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,6- Difluorophenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd509

b:0.1
occ:1.00
O4 A:BTB504 3.1 0.3 1.0
OD2 A:ASP384 3.2 0.6 1.0
O3 A:BTB504 3.3 0.2 1.0
O6 A:BTB504 3.6 0.4 1.0
OD1 A:ASP384 3.6 0.6 1.0
CG A:ASP384 3.7 90.7 1.0
C3 A:BTB504 3.9 1.0 1.0
C4 A:BTB504 4.4 0.4 1.0
C2 A:BTB504 4.5 0.9 1.0
N A:BTB504 4.6 0.0 1.0
C6 A:BTB504 4.6 0.9 1.0

Gadolinium binding site 2 out of 4 in 6nh6

Go back to Gadolinium Binding Sites List in 6nh6
Gadolinium binding site 2 out of 4 in the Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,6- Difluorophenethyl)-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 the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,6- Difluorophenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd508

b:48.0
occ:1.00
O4 B:BTB504 2.5 42.3 1.0
O B:HOH731 2.6 42.2 1.0
O B:THR319 2.6 58.3 1.0
O3 B:BTB504 2.7 48.5 1.0
OE1 B:GLU321 2.7 54.3 1.0
O C:HOH611 2.7 43.9 1.0
N B:BTB504 2.8 50.7 1.0
O8 B:BTB504 2.9 56.2 1.0
O6 B:BTB504 3.1 50.5 1.0
C6 B:BTB504 3.1 44.8 1.0
C8 B:BTB504 3.3 44.5 1.0
C2 B:BTB504 3.4 62.2 1.0
C5 B:BTB504 3.5 45.4 1.0
C3 B:BTB504 3.5 61.0 1.0
C4 B:BTB504 3.5 55.5 1.0
CD B:GLU321 3.6 54.6 1.0
C7 B:BTB504 3.6 47.7 1.0
OE2 B:GLU321 3.7 60.9 1.0
C B:THR319 3.7 52.1 1.0
CA B:THR319 4.4 43.3 1.0
OD1 C:ASP378 4.5 52.6 1.0
OD2 C:ASP378 4.6 54.0 1.0
N B:LEU320 4.6 55.2 1.0
CB B:THR319 4.6 39.7 1.0
CA B:LEU320 4.7 40.1 1.0
N B:GLU321 4.7 42.0 1.0
C1 B:BTB504 4.9 72.4 1.0
CG C:ASP378 5.0 43.4 1.0

Gadolinium binding site 3 out of 4 in 6nh6

Go back to Gadolinium Binding Sites List in 6nh6
Gadolinium binding site 3 out of 4 in the Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,6- Difluorophenethyl)-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 the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,6- Difluorophenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd511

b:0.4
occ:1.00
O4 C:BTB504 3.0 0.4 1.0
OD2 C:ASP384 3.1 99.8 1.0
O8 C:BTB504 3.4 0.7 1.0
CG C:ASP384 4.0 81.0 1.0
OD1 C:ASP384 4.0 89.5 1.0
C4 C:BTB504 4.1 0.2 1.0
C8 C:BTB504 4.2 0.9 1.0
C7 C:BTB504 4.2 0.4 1.0
N C:BTB504 4.6 0.6 1.0
O6 C:BTB507 4.6 71.6 1.0

Gadolinium binding site 4 out of 4 in 6nh6

Go back to Gadolinium Binding Sites List in 6nh6
Gadolinium binding site 4 out of 4 in the Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,6- Difluorophenethyl)-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 the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,6- Difluorophenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Gd508

b:48.6
occ:1.00
O4 D:BTB504 2.6 49.5 1.0
O D:THR319 2.6 32.3 1.0
OE1 D:GLU321 2.6 64.6 1.0
O3 D:BTB504 2.7 54.3 1.0
O D:HOH613 2.7 63.8 1.0
N D:BTB504 2.7 68.5 1.0
O6 D:BTB504 2.8 54.2 1.0
C6 D:BTB504 3.0 41.2 1.0
O8 D:BTB504 3.0 60.6 1.0
C5 D:BTB504 3.1 46.7 1.0
CD D:GLU321 3.4 64.8 1.0
C2 D:BTB504 3.5 77.1 1.0
OE2 D:GLU321 3.5 69.4 1.0
C3 D:BTB504 3.6 69.3 1.0
C8 D:BTB504 3.6 58.7 1.0
C4 D:BTB504 3.6 71.4 1.0
C7 D:BTB504 3.7 66.5 1.0
C D:THR319 3.7 63.8 1.0
CA D:THR319 4.4 50.2 1.0
CB D:THR319 4.5 44.7 1.0
N D:LEU320 4.7 54.3 1.0
N D:GLU321 4.7 41.4 1.0
CA D:LEU320 4.8 45.1 1.0
CG D:GLU321 4.9 46.5 1.0
C1 D:BTB504 4.9 77.8 1.0

Reference:

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
Page generated: Sun Dec 13 19:00:34 2020

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