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:
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
Go back to
Fluorine Binding Sites List in 6nh5
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
![](/pictures/F/pdb/nh/6nh5-F-sphere_01.jpg) Mono view
![](/pictures/F/pdb/nh/6nh5-F-sphere_01_stereo.jpg) 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
Go back to
Fluorine Binding Sites List in 6nh5
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
![](/pictures/F/pdb/nh/6nh5-F-sphere_02.jpg) Mono view
![](/pictures/F/pdb/nh/6nh5-F-sphere_02_stereo.jpg) 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
Go back to
Fluorine Binding Sites List in 6nh5
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
![](/pictures/F/pdb/nh/6nh5-F-sphere_03.jpg) Mono view
![](/pictures/F/pdb/nh/6nh5-F-sphere_03_stereo.jpg) 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
Go back to
Fluorine Binding Sites List in 6nh5
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
![](/pictures/F/pdb/nh/6nh5-F-sphere_04.jpg) Mono view
![](/pictures/F/pdb/nh/6nh5-F-sphere_04_stereo.jpg) 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
Go back to
Fluorine Binding Sites List in 6nh5
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
![](/pictures/F/pdb/nh/6nh5-F-sphere_05.jpg) Mono view
![](/pictures/F/pdb/nh/6nh5-F-sphere_05_stereo.jpg) 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
Go back to
Fluorine Binding Sites List in 6nh5
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
![](/pictures/F/pdb/nh/6nh5-F-sphere_06.jpg) Mono view
![](/pictures/F/pdb/nh/6nh5-F-sphere_06_stereo.jpg) 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
![](/pictures/F/pdb/nh/6nh5-F-sphere_07.jpg) Mono view
![](/pictures/F/pdb/nh/6nh5-F-sphere_07_stereo.jpg) 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
![](/pictures/F/pdb/nh/6nh5-F-sphere_08.jpg) Mono view
![](/pictures/F/pdb/nh/6nh5-F-sphere_08_stereo.jpg) 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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