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Fluorine in PDB 6nh5: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-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 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-2- Yl)Ethyl)Phenethyl)-4-Methylpyridin-2-Amine, PDB code: 6nh5 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) 88.71 / 1.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.528, 152.760, 108.980, 90.00, 90.76, 90.00
R / Rfree (%) 19.7 / 24.1

Other elements in 6nh5:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-2- Yl)Ethyl)Phenethyl)-4-Methylpyridin-2-Amine also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Iron (Fe) 4 atoms
Gadolinium (Gd) 2 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 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-2- Yl)Ethyl)Phenethyl)-4-Methylpyridin-2-Amine (pdb code 6nh5). 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-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-2- Yl)Ethyl)Phenethyl)-4-Methylpyridin-2-Amine, PDB code: 6nh5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6nh5

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Fluorine binding site 1 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-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 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-2- Yl)Ethyl)Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:0.9
occ:1.00
 F13 A:KLD503 0.0 0.9 1.0
C13 A:KLD503 1.3 0.2 1.0
O2A A:HEM501 2.2 0.5 1.0
C14 A:KLD503 2.4 0.8 1.0
C12 A:KLD503 2.4 0.3 1.0
CGA A:HEM501 3.3 0.2 1.0
N3 A:H4B502 3.4 95.6 1.0
O4 A:H4B502 3.5 0.5 1.0
C15 A:KLD503 3.6 0.6 1.0
C11 A:KLD503 3.6 97.9 1.0
CBA A:HEM501 3.7 87.7 1.0
C4 A:H4B502 3.9 98.8 1.0
C16 A:KLD503 4.1 0.6 1.0
CZ3 A:TRP447 4.2 56.2 1.0
NH1 A:ARG365 4.3 43.2 1.0
O1A A:HEM501 4.3 0.4 1.0
O A:HOH699 4.4 62.2 1.0
C2 A:H4B502 4.5 96.5 1.0
CH2 A:TRP447 4.6 55.4 1.0
N2 A:H4B502 4.7 89.3 1.0
C09 A:KLD503 4.9 83.9 1.0
C17 A:KLD503 4.9 0.6 1.0

Fluorine binding site 2 out of 8 in 6nh5

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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-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-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 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-2- Yl)Ethyl)Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:0.8
occ:1.00
 F23 A:KLD503 0.0 0.8 1.0
C23 A:KLD503 1.4 0.1 1.0
C22 A:KLD503 2.4 0.7 1.0
C24 A:KLD503 2.4 0.7 1.0
C18 A:KLD503 3.0 0.5 1.0
C25 A:KLD503 3.0 0.9 1.0
N21 A:KLD503 3.2 0.7 1.0
CZ A:PHE105 3.8 78.9 1.0
C21 A:KLD503 3.9 0.3 1.0
CE2 A:PHE105 4.3 74.3 1.0
C17 A:KLD503 4.5 0.6 1.0
CG1 A:VAL104 4.6 51.6 1.0
CE1 A:PHE105 4.7 77.0 1.0
CZ3 B:TRP74 4.9 59.9 1.0

Fluorine binding site 3 out of 8 in 6nh5

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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 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-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 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-2- Yl)Ethyl)Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:85.8
occ:1.00
 F13 B:KLD503 0.0 85.8 1.0
C13 B:KLD503 1.3 86.7 1.0
C12 B:KLD503 2.4 81.5 1.0
C14 B:KLD503 2.4 88.7 1.0
O1A B:HEM501 2.4 96.5 1.0
NH1 B:ARG365 2.6 76.8 1.0
CGA B:HEM501 3.3 92.3 1.0
CZ B:ARG365 3.4 62.9 1.0
CBA B:HEM501 3.5 69.4 1.0
N3 B:H4B502 3.6 69.9 1.0
C11 B:KLD503 3.6 69.3 1.0
C15 B:KLD503 3.6 87.2 1.0
O4 B:H4B502 3.7 83.3 1.0
CZ3 B:TRP447 3.8 45.7 1.0
CD B:ARG365 4.0 64.0 1.0
NE B:ARG365 4.1 56.1 1.0
C4 B:H4B502 4.1 76.8 1.0
C16 B:KLD503 4.1 75.3 1.0
NH2 B:ARG365 4.2 57.3 1.0
O2A B:HEM501 4.3 94.2 1.0
CH2 B:TRP447 4.4 42.1 1.0
CAA B:HEM501 4.5 39.3 1.0
CE3 B:TRP447 4.6 39.3 1.0
C2 B:H4B502 4.6 68.4 1.0
N2 B:H4B502 4.8 47.5 1.0
C09 B:KLD503 4.8 48.9 1.0
O B:HOH748 4.9 0.1 1.0
C17 B:KLD503 4.9 89.2 1.0
C18 B:KLD503 5.0 89.8 1.0

Fluorine binding site 4 out of 8 in 6nh5

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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-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-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 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-2- Yl)Ethyl)Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:0.1
occ:1.00
 F23 B:KLD503 0.0 0.1 1.0
C23 B:KLD503 1.4 0.1 1.0
C22 B:KLD503 2.3 0.3 1.0
C24 B:KLD503 2.4 0.1 1.0
O B:HOH776 3.0 64.3 1.0
C18 B:KLD503 3.1 89.8 1.0
C25 B:KLD503 3.1 98.8 1.0
N21 B:KLD503 3.3 0.1 1.0
C21 B:KLD503 4.1 0.0 1.0
CZ B:PHE105 4.4 58.4 1.0
C17 B:KLD503 4.6 89.2 1.0
O B:HOH733 4.6 52.8 1.0
CG1 B:VAL104 4.7 42.0 1.0
CZ3 A:TRP74 4.8 50.0 1.0
CE2 B:PHE105 4.9 46.3 1.0

Fluorine binding site 5 out of 8 in 6nh5

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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-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-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 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-2- Yl)Ethyl)Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F503

b:86.6
occ:1.00
 F13 C:KLD503 0.0 86.6 1.0
C13 C:KLD503 1.3 81.8 1.0
O2A C:HEM501 2.1 96.2 1.0
C14 C:KLD503 2.3 78.7 1.0
C12 C:KLD503 2.4 82.9 1.0
O4 C:H4B502 3.1 76.6 1.0
CGA C:HEM501 3.2 94.4 1.0
N3 C:H4B502 3.3 75.7 1.0
C15 C:KLD503 3.6 80.0 1.0
O C:HOH712 3.6 49.7 1.0
C4 C:H4B502 3.6 78.8 1.0
C11 C:KLD503 3.7 79.6 1.0
O C:HOH609 3.8 45.2 1.0
CBA C:HEM501 3.9 74.2 1.0
CZ3 C:TRP447 4.1 58.7 1.0
C16 C:KLD503 4.1 79.9 1.0
O1A C:HEM501 4.2 0.8 1.0
NH1 C:ARG365 4.3 33.8 1.0
C2 C:H4B502 4.4 76.9 1.0
CH2 C:TRP447 4.5 54.0 1.0
N2 C:H4B502 4.8 56.8 1.0
C17 C:KLD503 4.8 84.8 1.0
C18 C:KLD503 4.9 91.3 1.0
C09 C:KLD503 4.9 69.6 1.0
CE3 C:TRP447 4.9 50.7 1.0

Fluorine binding site 6 out of 8 in 6nh5

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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 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-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 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-2- Yl)Ethyl)Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F503

b:0.2
occ:1.00
 F23 C:KLD503 0.0 0.2 1.0
C23 C:KLD503 1.4 0.5 1.0
C22 C:KLD503 2.4 0.1 1.0
C24 C:KLD503 2.4 0.3 1.0
C18 C:KLD503 3.2 91.3 1.0
C25 C:KLD503 3.2 0.3 1.0
N21 C:KLD503 3.3 0.1 1.0
CZ C:PHE105 4.3 71.0 1.0
C17 C:KLD503 4.3 84.8 1.0
C21 C:KLD503 4.4 0.7 1.0
CE2 C:PHE105 4.8 67.8 1.0

Fluorine binding site 7 out of 8 in 6nh5

Go back to Fluorine Binding Sites List in 6nh5
Fluorine binding site 7 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-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 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-2- Yl)Ethyl)Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F502

b:70.6
occ:1.00
 F13 D:KLD502 0.0 70.6 1.0
C13 D:KLD502 1.3 74.9 1.0
C14 D:KLD502 2.4 77.8 1.0
C12 D:KLD502 2.4 73.5 1.0
O2A D:HEM501 3.3 99.9 1.0
CZ D:ARG365 3.5 56.6 1.0
NH1 D:ARG365 3.5 54.1 1.0
O4 C:H4B509 3.5 82.9 1.0
N3 C:H4B509 3.5 78.2 1.0
CBA D:HEM501 3.6 72.5 1.0
CGA D:HEM501 3.6 92.2 1.0
C15 D:KLD502 3.6 81.8 1.0
C11 D:KLD502 3.7 67.1 1.0
NE D:ARG365 3.7 51.0 1.0
CZ3 D:TRP447 3.8 49.2 1.0
CD D:ARG365 3.9 53.9 1.0
NH2 D:ARG365 4.0 61.6 1.0
C4 C:H4B509 4.0 80.2 1.0
C16 D:KLD502 4.1 75.1 1.0
CH2 D:TRP447 4.2 48.6 1.0
O1A D:HEM501 4.5 96.4 1.0
C2 C:H4B509 4.6 79.1 1.0
CE3 D:TRP447 4.7 41.4 1.0
N2 C:H4B509 4.8 80.2 1.0
C17 D:KLD502 4.9 82.2 1.0
C09 D:KLD502 4.9 53.3 1.0

Fluorine binding site 8 out of 8 in 6nh5

Go back to Fluorine Binding Sites List in 6nh5
Fluorine binding site 8 out of 8 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-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 6-(3-Fluoro-5-(2-((2R,4S)-4-Fluoro-1-Methylpyrrolidin-2- Yl)Ethyl)Phenethyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F502

b:0.1
occ:1.00
 F23 D:KLD502 0.0 0.1 1.0
C23 D:KLD502 1.4 0.8 1.0
C22 D:KLD502 2.4 0.5 1.0
C24 D:KLD502 2.4 99.9 1.0
C18 D:KLD502 3.1 87.1 1.0
C25 D:KLD502 3.2 96.6 1.0
N21 D:KLD502 3.4 0.2 1.0
O C:HOH718 3.6 64.0 1.0
CG1 D:VAL104 3.6 40.3 1.0
CZ D:PHE105 4.0 57.5 1.0
CE2 D:PHE105 4.1 51.6 1.0
C21 D:KLD502 4.5 0.9 1.0
C17 D:KLD502 4.6 82.2 1.0
CZ3 C:TRP74 4.7 62.2 1.0
O C:HOH631 4.8 68.6 1.0
CE1 D:PHE105 5.0 59.1 1.0
CH2 C:TRP74 5.0 63.5 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: Thu Aug 1 22:57:35 2024

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