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Fluorine 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:

Chlorine (Cl) 4 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms
Gadolinium (Gd) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 8 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7tsp

Go back to Fluorine Binding Sites List in 7tsp
Fluorine binding site 1 out of 8 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 Fluorine with other atoms in the F 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:F503

b:88.0
occ:1.00
 F17 A:K8O503 0.0 88.0 1.0
C14 A:K8O503 1.3 84.9 1.0
F18 A:K8O503 2.2 91.9 1.0
C13 A:K8O503 2.3 79.0 1.0
C15 A:K8O503 2.3 76.4 1.0
C12 A:K8O503 2.8 77.2 1.0
C16 A:K8O503 2.8 78.5 1.0
N11 A:K8O503 3.4 79.1 1.0
O2D A:HEM501 4.5 75.7 1.0
C10 A:K8O503 4.5 77.0 1.0
ND2 A:ASN338 4.6 80.1 1.0
CB A:SER246 4.9 60.7 1.0

Fluorine binding site 2 out of 8 in 7tsp

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Fluorine binding site 2 out of 8 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 Fluorine with other atoms in the F 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
A:F503

b:91.9
occ:1.00
 F18 A:K8O503 0.0 91.9 1.0
C14 A:K8O503 1.3 84.9 1.0
F17 A:K8O503 2.2 88.0 1.0
C15 A:K8O503 2.3 76.4 1.0
C13 A:K8O503 2.3 79.0 1.0
ND2 A:ASN338 3.0 80.1 1.0
CB A:SER246 3.4 60.7 1.0
CG A:ASN338 3.6 74.0 1.0
OD1 A:ASN338 3.6 68.8 1.0
O A:SER246 3.6 60.4 1.0
C12 A:K8O503 3.6 77.2 1.0
C16 A:K8O503 3.6 78.5 1.0
N11 A:K8O503 4.0 79.1 1.0
C A:SER246 4.1 64.2 1.0
OG A:SER246 4.1 68.0 1.0
CA A:SER246 4.1 59.7 1.0
CG1 A:VAL336 4.4 57.6 1.0
CB A:ASN338 4.8 73.3 1.0
CG A:GLN247 4.9 69.6 1.0

Fluorine binding site 3 out of 8 in 7tsp

Go back to Fluorine Binding Sites List in 7tsp
Fluorine binding site 3 out of 8 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 Fluorine with other atoms in the F 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:F503

b:78.7
occ:1.00
 F17 B:K8O503 0.0 78.7 1.0
C14 B:K8O503 1.3 75.6 1.0
F18 B:K8O503 2.1 83.8 1.0
C13 B:K8O503 2.3 69.4 1.0
C15 B:K8O503 2.4 68.1 1.0
C12 B:K8O503 3.0 69.9 1.0
C16 B:K8O503 3.0 60.6 1.0
N11 B:K8O503 3.6 63.2 1.0
ND2 B:ASN338 4.2 44.2 1.0
O2D B:HEM501 4.6 60.6 1.0
CB B:SER246 4.6 40.1 1.0
OD1 B:ASN338 4.7 43.7 1.0
C10 B:K8O503 4.8 59.6 1.0
O1 B:GOL506 4.8 70.6 1.0
CG B:ASN338 4.9 39.6 1.0

Fluorine binding site 4 out of 8 in 7tsp

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Fluorine binding site 4 out of 8 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 Fluorine with other atoms in the F 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
B:F503

b:83.8
occ:1.00
 F18 B:K8O503 0.0 83.8 1.0
C14 B:K8O503 1.3 75.6 1.0
F17 B:K8O503 2.1 78.7 1.0
C13 B:K8O503 2.3 69.4 1.0
C15 B:K8O503 2.3 68.1 1.0
CB B:SER246 3.0 40.1 1.0
OG B:SER246 3.4 44.1 1.0
O B:SER246 3.5 38.2 1.0
C12 B:K8O503 3.6 69.9 1.0
C16 B:K8O503 3.6 60.6 1.0
C B:SER246 3.7 26.4 1.0
ND2 B:ASN338 3.8 44.2 1.0
CA B:SER246 3.9 26.6 1.0
N11 B:K8O503 3.9 63.2 1.0
CG B:GLN247 4.0 24.8 1.0
OD1 B:ASN338 4.1 43.7 1.0
CG B:ASN338 4.2 39.6 1.0
NE2 B:GLN247 4.4 42.9 1.0
N B:GLN247 4.4 27.0 1.0
CD B:GLN247 4.7 37.4 1.0
NH1 B:ARG250 4.8 64.0 1.0
CG1 B:VAL336 4.9 31.1 1.0

Fluorine binding site 5 out of 8 in 7tsp

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Fluorine binding site 5 out of 8 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 Fluorine with other atoms in the F binding site number 5 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
C:F503

b:97.0
occ:1.00
 F17 C:K8O503 0.0 97.0 1.0
C14 C:K8O503 1.3 97.4 1.0
F18 C:K8O503 2.2 98.2 1.0
C13 C:K8O503 2.3 96.7 1.0
C15 C:K8O503 2.3 94.2 1.0
C12 C:K8O503 2.9 93.6 1.0
C16 C:K8O503 2.9 94.8 1.0
N11 C:K8O503 3.5 94.2 1.0
O C:HOH658 4.0 52.0 1.0
ND2 C:ASN338 4.2 66.6 1.0
C10 C:K8O503 4.6 90.0 1.0
O C:HOH698 4.6 50.2 1.0
OG C:SER246 4.6 51.6 1.0
CB C:SER246 4.7 50.8 1.0
OD1 C:ASN338 4.9 64.0 1.0
O2D C:HEM501 5.0 58.5 1.0
CG C:ASN338 5.0 63.9 1.0

Fluorine binding site 6 out of 8 in 7tsp

Go back to Fluorine Binding Sites List in 7tsp
Fluorine binding site 6 out of 8 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 Fluorine with other atoms in the F binding site number 6 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
C:F503

b:98.2
occ:1.00
 F18 C:K8O503 0.0 98.2 1.0
C14 C:K8O503 1.3 97.4 1.0
F17 C:K8O503 2.2 97.0 1.0
C13 C:K8O503 2.3 96.7 1.0
C15 C:K8O503 2.3 94.2 1.0
ND2 C:ASN338 3.0 66.6 1.0
CB C:SER246 3.2 50.8 1.0
O C:SER246 3.3 53.4 1.0
OG C:SER246 3.4 51.6 1.0
CG C:ASN338 3.5 63.9 1.0
OD1 C:ASN338 3.5 64.0 1.0
C16 C:K8O503 3.6 94.8 1.0
C12 C:K8O503 3.6 93.6 1.0
C C:SER246 3.8 58.5 1.0
O C:HOH658 3.9 52.0 1.0
CA C:SER246 3.9 59.1 1.0
N11 C:K8O503 4.0 94.2 1.0
CG C:GLN247 4.4 51.5 1.0
CG1 C:VAL336 4.4 48.3 1.0
CB C:ASN338 4.7 57.5 1.0
N C:GLN247 4.7 57.6 1.0
OE1 C:GLN247 4.9 63.6 1.0

Fluorine binding site 7 out of 8 in 7tsp

Go back to Fluorine Binding Sites List in 7tsp
Fluorine binding site 7 out of 8 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 Fluorine with other atoms in the F binding site number 7 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:F503

b:85.0
occ:1.00
 F17 D:K8O503 0.0 85.0 1.0
C14 D:K8O503 1.3 84.2 1.0
F18 D:K8O503 2.2 87.2 1.0
C13 D:K8O503 2.3 78.1 1.0
C15 D:K8O503 2.3 85.9 1.0
C12 D:K8O503 2.9 78.8 1.0
C16 D:K8O503 3.0 81.1 1.0
N11 D:K8O503 3.5 71.3 1.0
ND2 D:ASN338 4.6 41.9 1.0
CB D:SER246 4.6 43.9 1.0
C10 D:K8O503 4.6 59.7 1.0
OG D:SER246 4.8 51.8 1.0

Fluorine binding site 8 out of 8 in 7tsp

Go back to Fluorine Binding Sites List in 7tsp
Fluorine binding site 8 out of 8 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 Fluorine with other atoms in the F binding site number 8 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:F503

b:87.2
occ:1.00
 F18 D:K8O503 0.0 87.2 1.0
C14 D:K8O503 1.3 84.2 1.0
F17 D:K8O503 2.2 85.0 1.0
C15 D:K8O503 2.3 85.9 1.0
C13 D:K8O503 2.3 78.1 1.0
OG D:SER246 3.0 51.8 1.0
CB D:SER246 3.2 43.9 1.0
NH1 D:ARG250 3.4 56.4 1.0
C12 D:K8O503 3.6 78.8 1.0
C16 D:K8O503 3.6 81.1 1.0
N11 D:K8O503 4.0 71.3 1.0
CZ D:ARG250 4.2 66.4 1.0
CG D:GLN247 4.2 26.4 1.0
NE2 D:GLN247 4.3 42.0 1.0
C D:SER246 4.4 31.3 1.0
CA D:SER246 4.4 39.1 1.0
O D:SER246 4.5 38.5 1.0
CD D:GLN247 4.7 41.6 1.0
NH2 D:ARG250 4.8 82.1 1.0
ND2 D:ASN338 4.8 41.9 1.0
NE D:ARG250 4.9 63.0 1.0
N D:GLN247 4.9 32.6 1.0
CD D:ARG250 5.0 57.5 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: Fri Aug 2 13:39:47 2024

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