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Gadolinium in PDB 7tsp: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(4,4-Difluoropiperidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine

Enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(4,4-Difluoropiperidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine

All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(4,4-Difluoropiperidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-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-(3-(4,4-Difluoropiperidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine, PDB code: 7tsp 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) 39.02 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.471, 152.71, 108.781, 90, 90.62, 90
R / Rfree (%) 21.5 / 26.7

Other elements in 7tsp:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(4,4-Difluoropiperidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Chlorine (Cl) 4 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 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-(3-(4,4-Difluoropiperidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine (pdb code 7tsp). 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-(4,4-Difluoropiperidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine, PDB code: 7tsp:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 7tsp

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Gadolinium binding site 1 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(4,4-Difluoropiperidin-1-Yl)Prop-1-Yn-1-Yl)-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-(4,4-Difluoropiperidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd510

b:73.1
occ:0.67
 N A:BTB504 2.5 78.2 1.0
C4 A:BTB504 2.7 77.3 1.0
O4 A:BTB504 2.7 84.0 1.0
O3 A:BTB504 2.7 46.0 1.0
O A:HOH603 2.7 53.7 1.0
O6 A:BTB504 2.7 87.2 1.0
O A:HOH661 2.8 69.1 1.0
O8 A:BTB504 2.8 74.6 1.0
O A:HOH606 2.8 62.7 1.0
O A:HOH627 2.8 59.0 1.0
C2 A:BTB504 2.8 76.8 1.0
O A:HOH659 2.8 57.9 1.0
C3 A:BTB504 3.1 61.0 1.0
C5 A:BTB504 3.3 81.0 1.0
C6 A:BTB504 3.3 86.1 1.0
C7 A:BTB504 3.5 74.8 1.0
C8 A:BTB504 3.5 70.1 1.0
C1 A:BTB504 4.3 85.7 1.0
OD2 A:ASP384 4.5 68.9 1.0
OD1 A:ASP384 4.8 61.4 1.0

Gadolinium binding site 2 out of 4 in 7tsp

Go back to Gadolinium Binding Sites List in 7tsp
Gadolinium binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(4,4-Difluoropiperidin-1-Yl)Prop-1-Yn-1-Yl)-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-(4,4-Difluoropiperidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd508

b:49.7
occ:1.00
 O3 B:BTB504 2.4 33.9 1.0
O C:HOH603 2.6 50.9 1.0
O8 B:BTB504 2.6 53.4 1.0
O4 B:BTB504 2.6 60.4 1.0
N B:BTB504 2.6 38.7 1.0
O B:THR319 2.6 38.6 1.0
O B:HOH601 2.7 56.7 1.0
OE1 B:GLU321 2.7 55.9 1.0
O6 B:BTB504 2.8 54.8 1.0
C8 B:BTB504 3.2 49.4 1.0
C6 B:BTB504 3.2 45.9 1.0
C2 B:BTB504 3.2 58.2 1.0
C3 B:BTB504 3.2 54.1 1.0
C5 B:BTB504 3.3 30.3 1.0
C7 B:BTB504 3.4 41.2 1.0
C4 B:BTB504 3.5 64.8 1.0
CD B:GLU321 3.7 50.0 1.0
C B:THR319 3.7 55.0 1.0
OE2 B:GLU321 3.9 55.9 1.0
CA B:THR319 4.5 52.8 1.0
CB B:THR319 4.5 41.5 1.0
N B:GLU321 4.7 46.3 1.0
OD1 C:ASP378 4.7 54.0 1.0
N B:LEU320 4.7 49.7 1.0
CA B:LEU320 4.7 39.4 1.0
C1 B:BTB504 4.7 71.6 1.0
OD2 C:ASP378 4.7 54.5 1.0

Gadolinium binding site 3 out of 4 in 7tsp

Go back to Gadolinium Binding Sites List in 7tsp
Gadolinium binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(4,4-Difluoropiperidin-1-Yl)Prop-1-Yn-1-Yl)-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-(4,4-Difluoropiperidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd509

b:68.9
occ:0.69
 O3 C:BTB504 2.5 29.5 1.0
O4 C:BTB504 2.6 69.4 1.0
O C:HOH614 2.6 54.9 1.0
N C:BTB504 2.7 67.0 1.0
O6 C:BTB504 2.7 78.9 1.0
O8 C:BTB504 2.7 59.5 1.0
O B:HOH657 2.7 68.2 1.0
O C:HOH693 2.8 67.6 1.0
C3 C:BTB504 2.8 20.3 1.0
C2 C:BTB504 3.0 59.1 1.0
C4 C:BTB504 3.2 70.1 1.0
C6 C:BTB504 3.5 69.5 1.0
C7 C:BTB504 3.5 66.2 1.0
C8 C:BTB504 3.7 66.2 1.0
C5 C:BTB504 3.7 64.5 1.0
OD2 C:ASP384 4.1 75.9 1.0
O B:HOH737 4.4 79.5 1.0
C1 C:BTB504 4.5 68.4 1.0
OD1 B:ASP378 4.5 81.3 1.0
OD2 B:ASP378 4.7 76.1 1.0
OD1 C:ASP384 4.9 76.1 1.0
CG C:ASP384 4.9 71.9 1.0
CG B:ASP378 5.0 69.0 1.0

Gadolinium binding site 4 out of 4 in 7tsp

Go back to Gadolinium Binding Sites List in 7tsp
Gadolinium binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(4,4-Difluoropiperidin-1-Yl)Prop-1-Yn-1-Yl)-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-(4,4-Difluoropiperidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Gd508

b:50.6
occ:1.00
 O3 D:BTB504 2.4 40.3 1.0
O D:THR319 2.6 29.3 1.0
O8 D:BTB504 2.6 72.8 1.0
OE1 D:GLU321 2.6 61.2 1.0
O4 D:BTB504 2.7 70.5 1.0
O6 D:BTB504 2.8 36.3 1.0
N D:BTB504 2.8 69.8 1.0
C6 D:BTB504 3.1 38.8 1.0
C8 D:BTB504 3.4 65.1 1.0
C3 D:BTB504 3.4 60.7 1.0
C2 D:BTB504 3.4 75.7 1.0
C7 D:BTB504 3.5 66.6 1.0
C5 D:BTB504 3.5 53.9 1.0
CD D:GLU321 3.6 59.0 1.0
C4 D:BTB504 3.6 71.6 1.0
C D:THR319 3.8 53.8 1.0
OE2 D:GLU321 3.8 63.9 1.0
CA D:THR319 4.5 45.8 1.0
CB D:THR319 4.6 41.0 1.0
N D:GLU321 4.6 51.6 1.0
N D:LEU320 4.8 51.8 1.0
CA D:LEU320 4.8 47.0 1.0
CG D:GLU321 4.9 52.5 1.0
C1 D:BTB504 4.9 80.5 1.0

Reference:

D.Vasu, H.Li, C.D.Hardy, T.L.Poulos, R.B.Silverman. 2-Aminopyridines with A Shortened Amino Sidechain As Potent, Selective, and Highly Permeable Human Neuronal Nitric Oxide Synthase Inhibitors. Bioorg.Med.Chem. V. 69 16878 2022.
ISSN: ESSN 1464-3391
PubMed: 35772285
DOI: 10.1016/J.BMC.2022.116878
Page generated: Sat Aug 10 22:46:08 2024

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