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Gadolinium in PDB 8fgp: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methoxypyridin-2-Amine

Enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methoxypyridin-2-Amine

All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methoxypyridin-2-Amine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methoxypyridin-2-Amine, PDB code: 8fgp was solved by H.Li, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.25 / 1.88
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.091, 152.185, 108.685, 90, 90.9, 90
R / Rfree (%) 19.1 / 22.9

Other elements in 8fgp:

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

Iron (Fe) 4 atoms
Fluorine (F) 8 atoms
Zinc (Zn) 2 atoms
Chlorine (Cl) 4 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-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methoxypyridin-2-Amine (pdb code 8fgp). 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-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methoxypyridin-2-Amine, PDB code: 8fgp:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 8fgp

Go back to Gadolinium Binding Sites List in 8fgp
Gadolinium binding site 1 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methoxypyridin-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-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methoxypyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd510

b:115.8
occ:0.57
 O4 A:BTB504 2.7 101.2 1.0
O A:HOH649 2.7 83.9 1.0
O A:HOH709 2.8 79.7 1.0
O3 A:BTB504 2.8 90.7 1.0
O8 A:BTB504 2.8 112.5 1.0
N A:BTB504 3.1 108.3 1.0
O6 A:BTB504 3.1 102.8 1.0
O A:HOH702 3.1 65.5 1.0
C3 A:BTB504 3.4 96.1 1.0
C2 A:BTB504 3.5 101.9 1.0
C4 A:BTB504 3.6 103.0 1.0
O A:HOH625 3.9 66.2 1.0
C7 A:BTB504 3.9 107.1 1.0
C8 A:BTB504 3.9 107.8 1.0
C5 A:BTB504 4.0 107.8 1.0
C6 A:BTB504 4.0 105.6 1.0
OD1 A:ASP384 4.7 95.1 1.0
OD2 A:ASP384 4.8 98.9 1.0

Gadolinium binding site 2 out of 4 in 8fgp

Go back to Gadolinium Binding Sites List in 8fgp
Gadolinium binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methoxypyridin-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-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methoxypyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd508

b:42.1
occ:1.00
 O B:THR319 2.5 35.7 1.0
O4 B:BTB504 2.5 42.3 1.0
OE1 B:GLU321 2.7 55.0 1.0
O B:HOH767 2.7 63.7 1.0
O3 B:BTB504 2.7 62.5 1.0
O C:HOH603 2.7 36.6 1.0
O8 B:BTB504 2.7 50.0 1.0
N B:BTB504 2.8 47.8 1.0
O6 B:BTB504 2.9 62.4 1.0
C6 B:BTB504 3.2 57.9 1.0
C8 B:BTB504 3.2 44.1 1.0
C2 B:BTB504 3.4 66.7 1.0
CD B:GLU321 3.4 57.6 1.0
OE2 B:GLU321 3.5 63.1 1.0
C7 B:BTB504 3.5 43.9 1.0
C4 B:BTB504 3.5 58.6 1.0
C3 B:BTB504 3.5 68.0 1.0
C5 B:BTB504 3.5 60.2 1.0
C B:THR319 3.7 48.2 1.0
O C:HOH742 4.4 57.5 1.0
OD2 C:ASP378 4.5 46.6 1.0
CA B:THR319 4.5 40.0 1.0
OD1 C:ASP378 4.5 45.8 1.0
CA B:LEU320 4.6 40.4 1.0
N B:GLU321 4.6 37.8 1.0
N B:LEU320 4.6 46.6 1.0
CB B:THR319 4.7 43.2 1.0
CG B:GLU321 4.9 51.0 1.0
C1 B:BTB504 4.9 76.0 1.0
CG C:ASP378 5.0 51.0 1.0

Gadolinium binding site 3 out of 4 in 8fgp

Go back to Gadolinium Binding Sites List in 8fgp
Gadolinium binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methoxypyridin-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-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methoxypyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd509

b:72.1
occ:0.46
 O3 C:BTB504 2.6 46.4 1.0
O4 C:BTB504 2.7 71.9 1.0
O C:HOH702 2.8 71.7 1.0
O6 C:BTB504 2.8 100.2 1.0
O C:HOH754 2.8 79.5 1.0
O8 C:BTB504 2.8 82.5 1.0
O C:HOH711 2.8 98.2 1.0
N C:BTB504 3.0 92.1 1.0
C3 C:BTB504 3.4 65.4 1.0
C2 C:BTB504 3.4 82.2 1.0
C4 C:BTB504 3.5 80.5 1.0
C6 C:BTB504 3.7 96.8 1.0
C7 C:BTB504 3.7 87.8 1.0
C8 C:BTB504 3.8 81.8 1.0
C5 C:BTB504 3.9 90.6 1.0
C1 C:BTB504 4.9 74.5 1.0

Gadolinium binding site 4 out of 4 in 8fgp

Go back to Gadolinium Binding Sites List in 8fgp
Gadolinium binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methoxypyridin-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-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methoxypyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Gd507

b:48.3
occ:1.00
 O D:THR319 2.4 32.7 1.0
O D:HOH778 2.5 50.0 1.0
O4 D:BTB504 2.6 59.7 1.0
OE1 D:GLU321 2.7 62.5 1.0
O6 D:BTB504 2.7 46.1 1.0
N D:BTB504 2.8 79.5 1.0
O8 D:BTB504 2.8 72.5 1.0
C6 D:BTB504 2.8 52.3 1.0
O3 D:BTB504 2.9 61.9 1.0
C4 D:BTB504 3.2 69.2 1.0
C5 D:BTB504 3.4 68.1 1.0
C2 D:BTB504 3.4 80.4 1.0
C8 D:BTB504 3.4 79.1 1.0
CD D:GLU321 3.5 65.4 1.0
OE2 D:GLU321 3.6 74.3 1.0
C D:THR319 3.6 47.5 1.0
C7 D:BTB504 3.7 79.4 1.0
C3 D:BTB504 3.7 73.2 1.0
CA D:THR319 4.4 39.8 1.0
N D:LEU320 4.6 43.0 1.0
CA D:LEU320 4.6 46.0 1.0
CB D:THR319 4.6 48.3 1.0
N D:GLU321 4.6 39.2 1.0
C1 D:BTB504 4.8 84.1 1.0
O D:HOH721 4.9 50.5 1.0
CG D:GLU321 4.9 51.9 1.0

Reference:

D.Vasu, H.T.Do, H.Li, C.D.Hardy, A.Awasthi, T.L.Poulos, R.B.Silverman. Potent, Selective, and Membrane Permeable 2-Amino-4-Substituted Pyridine-Based Neuronal Nitric Oxide Synthase Inhibitors. J.Med.Chem. V. 66 9934 2023.
ISSN: ISSN 0022-2623
PubMed: 37433128
DOI: 10.1021/ACS.JMEDCHEM.3C00782
Page generated: Fri Aug 8 08:47:33 2025

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