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Gadolinium in PDB 6nh7: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,5,6- Trifluorophenethyl)-4-Methylpyridin-2-Amine

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,5,6- Trifluorophenethyl)-4-Methylpyridin-2-Amine, PDB code: 6nh7 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) 76.74 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.959, 109.381, 153.470, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.8

Other elements in 6nh7:

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

Fluorine (F) 12 atoms
Zinc (Zn) 1 atom
Iron (Fe) 2 atoms

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,5,6- Trifluorophenethyl)-4-Methylpyridin-2-Amine (pdb code 6nh7). 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-(3-(Dimethylamino)Propyl)-2,5,6- Trifluorophenethyl)-4-Methylpyridin-2-Amine, PDB code: 6nh7:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 6nh7

Go back to Gadolinium Binding Sites List in 6nh7
Gadolinium binding site 1 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,5,6- 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-(3-(3-(Dimethylamino)Propyl)-2,5,6- Trifluorophenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd509

b:85.1
occ:0.84
O8 A:BTB504 2.8 0.0 1.0
O4 A:BTB504 2.8 99.1 1.0
O A:HOH679 2.8 72.7 1.0
O A:HOH607 2.8 75.7 1.0
O6 A:BTB504 2.8 1.0 1.0
N A:BTB504 2.9 0.0 1.0
C6 A:BTB504 3.0 0.3 1.0
C8 A:BTB504 3.1 99.7 1.0
O A:HOH706 3.3 84.3 1.0
O3 A:BTB504 3.6 95.9 1.0
C7 A:BTB504 3.6 0.7 1.0
C5 A:BTB504 3.6 0.2 1.0
C2 A:BTB504 3.8 0.3 1.0
C4 A:BTB504 3.8 0.9 1.0
C3 A:BTB504 4.1 1.0 1.0
OD2 A:ASP384 4.4 85.0 1.0
OD1 A:ASP384 4.6 82.6 1.0
CG A:ASP384 5.0 75.8 1.0

Gadolinium binding site 2 out of 4 in 6nh7

Go back to Gadolinium Binding Sites List in 6nh7
Gadolinium binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,5,6- 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-(3-(3-(Dimethylamino)Propyl)-2,5,6- Trifluorophenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd510

b:49.4
occ:0.64
O A:HOH661 2.7 47.5 1.0
O A:HOH696 2.7 50.8 1.0
OE1 A:GLU156 2.7 93.1 1.0
OE1 A:GLN164 2.8 0.8 1.0
NE2 A:GLN164 2.8 0.7 1.0
CD A:GLN164 3.0 99.2 1.0
CD A:GLU156 3.4 91.3 1.0
OE2 A:GLU156 3.5 84.7 1.0
CG A:GLN164 4.2 84.0 1.0
CB A:GLN164 4.6 71.1 1.0
CG A:GLU156 4.8 93.6 1.0

Gadolinium binding site 3 out of 4 in 6nh7

Go back to Gadolinium Binding Sites List in 6nh7
Gadolinium binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,5,6- 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-(3-(3-(Dimethylamino)Propyl)-2,5,6- Trifluorophenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd507

b:45.5
occ:1.00
O B:THR319 2.5 33.8 1.0
O B:HOH683 2.6 53.0 1.0
O4 B:BTB504 2.6 63.2 1.0
OE1 B:GLU321 2.7 59.2 1.0
O3 B:BTB504 2.7 63.2 1.0
O8 B:BTB504 2.8 72.6 1.0
O6 B:BTB504 2.8 59.4 1.0
O B:HOH601 2.8 73.0 1.0
C6 B:BTB504 2.9 58.0 1.0
N B:BTB504 2.9 72.1 1.0
C5 B:BTB504 3.4 63.1 1.0
CD B:GLU321 3.5 57.7 1.0
OE2 B:GLU321 3.5 66.8 1.0
C2 B:BTB504 3.6 79.5 1.0
C4 B:BTB504 3.7 72.1 1.0
C8 B:BTB504 3.7 76.4 1.0
C3 B:BTB504 3.7 73.0 1.0
C B:THR319 3.7 46.9 1.0
C7 B:BTB504 3.8 77.8 1.0
CA B:THR319 4.4 48.7 1.0
O B:HOH627 4.6 46.4 1.0
CB B:THR319 4.6 50.1 1.0
N B:GLU321 4.6 36.5 1.0
N B:LEU320 4.7 46.1 1.0
CA B:LEU320 4.7 34.4 1.0
CG B:GLU321 4.9 42.5 1.0

Gadolinium binding site 4 out of 4 in 6nh7

Go back to Gadolinium Binding Sites List in 6nh7
Gadolinium binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3-(Dimethylamino)Propyl)-2,5,6- 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-(3-(3-(Dimethylamino)Propyl)-2,5,6- Trifluorophenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd508

b:59.8
occ:0.61
O6 B:BTB505 2.7 90.2 1.0
O B:HOH643 2.8 52.1 1.0
O8 B:BTB505 2.8 74.9 1.0
O B:HOH736 2.9 68.2 1.0
N B:BTB505 3.0 80.3 1.0
C8 B:BTB505 3.2 68.5 1.0
C7 B:BTB505 3.3 70.6 1.0
C5 B:BTB505 3.3 88.1 1.0
C6 B:BTB505 3.4 90.7 1.0
O4 B:BTB505 3.4 52.1 1.0
O B:HOH602 3.5 55.7 1.0
O B:HOH604 4.0 68.2 1.0
C2 B:BTB505 4.3 76.5 1.0
C4 B:BTB505 4.4 63.9 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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