Fluorine in PDB 6nh3: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine, PDB code: 6nh3 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) 88.87 / 2.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.469, 153.089, 109.150, 90.00, 90.80, 90.00
R / Rfree (%) 20.6 / 25.7

Other elements in 6nh3:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine also contains other interesting chemical elements:

Zinc (Zn) 6 atoms
Iron (Fe) 4 atoms
Gadolinium (Gd) 4 atoms
Chlorine (Cl) 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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine (pdb code 6nh3). 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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine, PDB code: 6nh3:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6nh3

Go back to Fluorine Binding Sites List in 6nh3
Fluorine binding site 1 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:77.9
occ:1.00
F13 A:KL4502 0.0 77.9 1.0
C13 A:KL4502 1.3 78.3 1.0
C12 A:KL4502 2.4 77.2 1.0
C14 A:KL4502 2.4 77.8 1.0
CZ3 A:TRP447 3.3 50.7 1.0
NH1 A:ARG365 3.4 61.4 1.0
O1A A:HEM501 3.5 87.0 1.0
O B:HOH1051 3.6 44.7 1.0
CZ A:ARG365 3.6 64.2 1.0
C11 A:KL4502 3.6 72.0 1.0
C15 A:KL4502 3.7 77.2 1.0
CH2 A:TRP447 3.8 54.9 1.0
NE A:ARG365 3.9 61.4 1.0
C12 B:KL4801 4.0 69.8 1.0
C16 A:KL4502 4.1 77.1 1.0
CE3 A:TRP447 4.1 52.7 1.0
CD A:ARG365 4.1 61.9 1.0
NH2 A:ARG365 4.2 68.4 1.0
F13 B:KL4801 4.3 76.8 1.0
CAA A:HEM501 4.4 51.8 1.0
CGA A:HEM501 4.4 80.2 1.0
O A:HOH686 4.5 34.8 1.0
C13 B:KL4801 4.5 74.0 1.0
CBA A:HEM501 4.8 63.7 1.0
CZ2 A:TRP447 4.9 60.2 1.0
C09 A:KL4502 4.9 58.8 1.0
C11 B:KL4801 4.9 59.6 1.0
C17 A:KL4502 4.9 76.3 1.0

Fluorine binding site 2 out of 8 in 6nh3

Go back to Fluorine Binding Sites List in 6nh3
Fluorine binding site 2 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F509

b:48.9
occ:1.00
F13 A:KL4509 0.0 48.9 1.0
C13 A:KL4509 1.3 52.6 1.0
C12 A:KL4509 2.4 51.3 1.0
C14 A:KL4509 2.4 53.2 1.0
CD B:ARG365 3.4 34.6 1.0
C14 B:KL4803 3.5 61.7 1.0
O B:HOH923 3.5 35.2 1.0
C11 A:KL4509 3.6 51.3 1.0
C15 A:KL4509 3.7 56.0 1.0
O B:HOH1042 3.7 22.6 1.0
NE B:ARG365 4.0 37.4 1.0
C13 B:KL4803 4.0 62.1 1.0
F13 B:KL4803 4.0 66.0 1.0
C16 A:KL4509 4.1 54.9 1.0
C15 B:KL4803 4.2 65.5 1.0
C17 B:KL4803 4.5 67.7 1.0
CG B:ARG365 4.5 34.7 1.0
NH1 B:ARG372 4.5 25.1 1.0
O B:HOH985 4.6 32.9 1.0
CZ B:ARG365 4.9 39.1 1.0
C09 A:KL4509 4.9 47.1 1.0
C18 B:KL4803 4.9 65.0 1.0
C17 A:KL4509 4.9 53.1 1.0

Fluorine binding site 3 out of 8 in 6nh3

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Fluorine binding site 3 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:76.8
occ:1.00
F13 B:KL4801 0.0 76.8 1.0
C13 B:KL4801 1.3 74.0 1.0
C12 B:KL4801 2.4 69.8 1.0
C14 B:KL4801 2.4 66.8 1.0
O A:HOH654 3.2 42.3 1.0
C11 B:KL4801 3.6 59.6 1.0
C15 B:KL4801 3.7 66.6 1.0
C14 A:KL4502 3.7 77.8 1.0
CD A:ARG365 3.8 61.9 1.0
NH1 A:ARG372 3.8 52.4 1.0
NE A:ARG365 4.1 61.4 1.0
C16 B:KL4801 4.1 60.4 1.0
C13 A:KL4502 4.2 78.3 1.0
C18 A:KL4502 4.3 81.7 1.0
F13 A:KL4502 4.3 77.9 1.0
O A:HOH677 4.3 30.2 1.0
C15 A:KL4502 4.4 77.2 1.0
CG A:ARG365 4.7 52.9 1.0
C17 A:KL4502 4.7 76.3 1.0
C09 B:KL4801 4.9 59.2 1.0
C17 B:KL4801 4.9 73.0 1.0

Fluorine binding site 4 out of 8 in 6nh3

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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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:66.0
occ:1.00
F13 B:KL4803 0.0 66.0 1.0
C13 B:KL4803 1.3 62.1 1.0
C14 B:KL4803 2.4 61.7 1.0
C12 B:KL4803 2.4 59.1 1.0
O2A B:HEM802 3.0 77.1 1.0
NH1 B:ARG365 3.2 34.8 1.0
O A:HOH684 3.3 45.8 1.0
CZ3 B:TRP447 3.5 42.7 1.0
CZ B:ARG365 3.5 39.1 1.0
C15 B:KL4803 3.6 65.5 1.0
C11 B:KL4803 3.7 53.3 1.0
CGA B:HEM802 3.7 69.6 1.0
NE B:ARG365 3.9 37.4 1.0
CD B:ARG365 4.0 34.6 1.0
CH2 B:TRP447 4.0 41.4 1.0
F13 A:KL4509 4.0 48.9 1.0
O B:HOH1044 4.1 41.5 1.0
NH2 B:ARG365 4.2 39.7 1.0
C12 A:KL4509 4.2 51.3 1.0
C16 B:KL4803 4.2 55.9 1.0
CE3 B:TRP447 4.3 35.4 1.0
CAA B:HEM802 4.4 32.1 1.0
CBA B:HEM802 4.4 55.8 1.0
O1A B:HEM802 4.5 72.4 1.0
C13 A:KL4509 4.5 52.6 1.0
C17 B:KL4803 4.9 67.7 1.0
C09 B:KL4803 4.9 34.0 1.0
C18 B:KL4803 4.9 65.0 1.0

Fluorine binding site 5 out of 8 in 6nh3

Go back to Fluorine Binding Sites List in 6nh3
Fluorine binding site 5 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:55.1
occ:1.00
F13 C:KL4502 0.0 55.1 1.0
C13 C:KL4502 1.3 55.3 1.0
C14 C:KL4502 2.3 56.5 1.0
C12 C:KL4502 2.4 59.3 1.0
O2A C:HEM501 2.6 0.3 1.0
O C:HOH708 3.2 52.5 1.0
NH1 C:ARG365 3.3 52.9 1.0
CZ C:ARG365 3.4 61.0 1.0
NE C:ARG365 3.5 63.1 1.0
C15 C:KL4502 3.6 67.8 1.0
C11 C:KL4502 3.6 62.9 1.0
CD C:ARG365 3.7 66.5 1.0
F13 C:KL4503 3.7 74.0 1.0
C12 C:KL4503 3.8 79.4 1.0
CZ3 C:TRP447 3.9 56.2 1.0
CGA C:HEM501 3.9 0.8 1.0
NH2 C:ARG365 4.0 66.9 1.0
C16 C:KL4502 4.1 68.0 1.0
C13 C:KL4503 4.2 78.8 1.0
CH2 C:TRP447 4.3 53.6 1.0
CE3 C:TRP447 4.6 51.6 1.0
O1A C:HEM501 4.7 0.3 1.0
O C:HOH712 4.7 31.7 1.0
C18 C:KL4502 4.8 70.0 1.0
CAA C:HEM501 4.8 59.5 1.0
CBA C:HEM501 4.8 84.0 1.0
C17 C:KL4502 4.8 71.1 1.0
C09 C:KL4502 4.9 57.5 1.0
C11 C:KL4503 4.9 73.8 1.0

Fluorine binding site 6 out of 8 in 6nh3

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Fluorine binding site 6 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F503

b:74.0
occ:1.00
F13 C:KL4503 0.0 74.0 1.0
C13 C:KL4503 1.3 78.8 1.0
C12 C:KL4503 2.4 79.4 1.0
C14 C:KL4503 2.4 80.9 1.0
C14 C:KL4502 3.4 56.5 1.0
O C:HOH633 3.5 40.0 1.0
C11 C:KL4503 3.6 73.8 1.0
CD C:ARG365 3.6 66.5 1.0
C15 C:KL4503 3.7 81.2 1.0
F13 C:KL4502 3.7 55.1 1.0
C13 C:KL4502 3.8 55.3 1.0
NE C:ARG365 3.9 63.1 1.0
C16 C:KL4503 4.1 75.7 1.0
C15 C:KL4502 4.2 67.8 1.0
NH1 C:ARG372 4.3 35.7 1.0
O C:HOH694 4.3 25.0 1.0
C17 C:KL4502 4.6 71.1 1.0
O C:HOH672 4.6 52.1 1.0
CG C:ARG365 4.7 55.3 1.0
C18 C:KL4502 4.7 70.0 1.0
C09 C:KL4503 4.9 67.8 1.0
CZ C:ARG365 4.9 61.0 1.0
C17 C:KL4503 4.9 80.9 1.0
C12 C:KL4502 4.9 59.3 1.0

Fluorine binding site 7 out of 8 in 6nh3

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Fluorine binding site 7 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F511

b:55.0
occ:1.00
F13 C:KL4511 0.0 55.0 1.0
C13 C:KL4511 1.3 55.6 1.0
C12 C:KL4511 2.4 52.1 1.0
C14 C:KL4511 2.4 57.4 1.0
O D:HOH703 3.4 46.2 1.0
CD D:ARG365 3.4 37.6 1.0
C14 D:KL4502 3.5 53.8 1.0
C11 C:KL4511 3.6 49.4 1.0
C15 C:KL4511 3.7 52.9 1.0
O D:HOH762 3.8 24.6 1.0
F13 D:KL4502 3.9 57.0 1.0
NE D:ARG365 3.9 33.3 1.0
C13 D:KL4502 4.0 54.4 1.0
O D:HOH760 4.1 37.3 1.0
C16 C:KL4511 4.1 43.6 1.0
NH1 D:ARG372 4.3 33.0 1.0
C15 D:KL4502 4.3 63.4 1.0
CG D:ARG365 4.5 38.2 1.0
C18 D:KL4502 4.6 64.4 1.0
O D:HOH722 4.6 51.2 1.0
C17 D:KL4502 4.7 63.2 1.0
CZ D:ARG365 4.8 38.1 1.0
C09 C:KL4511 4.9 47.8 1.0
O D:HOH780 4.9 54.6 1.0
C17 C:KL4511 4.9 59.3 1.0

Fluorine binding site 8 out of 8 in 6nh3

Go back to Fluorine Binding Sites List in 6nh3
Fluorine binding site 8 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F502

b:57.0
occ:1.00
F13 D:KL4502 0.0 57.0 1.0
C13 D:KL4502 1.3 54.4 1.0
C14 D:KL4502 2.4 53.8 1.0
C12 D:KL4502 2.4 48.1 1.0
NH1 D:ARG365 3.2 40.5 1.0
CZ3 D:TRP447 3.4 39.9 1.0
CZ D:ARG365 3.5 38.1 1.0
O1A D:HEM501 3.6 62.8 1.0
C15 D:KL4502 3.6 63.4 1.0
C11 D:KL4502 3.7 51.7 1.0
NE D:ARG365 3.8 33.3 1.0
C12 C:KL4511 3.9 52.1 1.0
O C:HOH699 3.9 53.9 1.0
CH2 D:TRP447 3.9 40.9 1.0
F13 C:KL4511 3.9 55.0 1.0
CD D:ARG365 3.9 37.6 1.0
CGA D:HEM501 4.0 58.8 1.0
C16 D:KL4502 4.1 59.4 1.0
NH2 D:ARG365 4.2 35.0 1.0
CE3 D:TRP447 4.2 33.1 1.0
C13 C:KL4511 4.3 55.6 1.0
O D:HOH773 4.3 33.6 1.0
O C:HOH698 4.4 41.8 1.0
CBA D:HEM501 4.5 48.8 1.0
O2A D:HEM501 4.5 64.5 1.0
CAA D:HEM501 4.6 38.6 1.0
C18 D:KL4502 4.8 64.4 1.0
C17 D:KL4502 4.8 63.2 1.0
C11 C:KL4511 4.9 49.4 1.0
C09 D:KL4502 4.9 30.8 1.0
CZ2 D:TRP447 4.9 37.0 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 13:00:22 2020

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