Iron in PDB 8fgq: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine
Enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine
All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine:
1.14.13.39;
Protein crystallography data
The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine, PDB code: 8fgq
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)
|
75.78 /
2.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
59.569,
151.48,
108.348,
90,
91.08,
90
|
R / Rfree (%)
|
19.3 /
24.6
|
Other elements in 8fgq:
The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine
(pdb code 8fgq). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine, PDB code: 8fgq:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 8fgq
Go back to
Iron Binding Sites List in 8fgq
Iron binding site 1 out
of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine
![](/pictures/FE/pdb/fg/8fgq-FE-sphere_01.jpg) Mono view
![](/pictures/FE/pdb/fg/8fgq-FE-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:38.0
occ:1.00
|
FE
|
A:HEM501
|
0.0
|
38.0
|
1.0
|
NC
|
A:HEM501
|
2.1
|
48.9
|
1.0
|
ND
|
A:HEM501
|
2.1
|
48.5
|
1.0
|
NA
|
A:HEM501
|
2.1
|
46.0
|
1.0
|
NB
|
A:HEM501
|
2.1
|
49.4
|
1.0
|
SG
|
A:CYS184
|
2.2
|
28.3
|
1.0
|
C4D
|
A:HEM501
|
3.1
|
51.1
|
1.0
|
C1C
|
A:HEM501
|
3.1
|
48.0
|
1.0
|
C4B
|
A:HEM501
|
3.1
|
51.9
|
1.0
|
C4C
|
A:HEM501
|
3.1
|
54.7
|
1.0
|
C1D
|
A:HEM501
|
3.1
|
57.3
|
1.0
|
C1A
|
A:HEM501
|
3.1
|
44.5
|
1.0
|
C1B
|
A:HEM501
|
3.1
|
51.0
|
1.0
|
C4A
|
A:HEM501
|
3.1
|
49.5
|
1.0
|
CB
|
A:CYS184
|
3.3
|
27.3
|
1.0
|
CHA
|
A:HEM501
|
3.4
|
45.2
|
1.0
|
CHC
|
A:HEM501
|
3.4
|
46.6
|
1.0
|
CHD
|
A:HEM501
|
3.5
|
57.2
|
1.0
|
CHB
|
A:HEM501
|
3.5
|
49.2
|
1.0
|
C05
|
A:V80503
|
4.0
|
53.1
|
1.0
|
CA
|
A:CYS184
|
4.0
|
28.6
|
1.0
|
C04
|
A:V80503
|
4.0
|
44.3
|
1.0
|
C06
|
A:V80503
|
4.2
|
54.0
|
1.0
|
N03
|
A:V80503
|
4.3
|
45.3
|
1.0
|
C3D
|
A:HEM501
|
4.3
|
59.5
|
1.0
|
C3B
|
A:HEM501
|
4.3
|
55.1
|
1.0
|
C2C
|
A:HEM501
|
4.3
|
52.8
|
1.0
|
C2B
|
A:HEM501
|
4.3
|
53.1
|
1.0
|
C3C
|
A:HEM501
|
4.3
|
56.1
|
1.0
|
C2D
|
A:HEM501
|
4.3
|
58.7
|
1.0
|
C2A
|
A:HEM501
|
4.3
|
49.9
|
1.0
|
C3A
|
A:HEM501
|
4.4
|
51.3
|
1.0
|
C07
|
A:V80503
|
4.5
|
38.6
|
1.0
|
N01
|
A:V80503
|
4.5
|
50.6
|
1.0
|
C02
|
A:V80503
|
4.5
|
44.6
|
1.0
|
NE1
|
A:TRP178
|
4.6
|
55.7
|
1.0
|
C
|
A:CYS184
|
4.8
|
28.8
|
1.0
|
N
|
A:GLY186
|
4.9
|
38.5
|
1.0
|
C08
|
A:V80503
|
4.9
|
62.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 8fgq
Go back to
Iron Binding Sites List in 8fgq
Iron binding site 2 out
of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine
![](/pictures/FE/pdb/fg/8fgq-FE-sphere_02.jpg) Mono view
![](/pictures/FE/pdb/fg/8fgq-FE-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:20.4
occ:1.00
|
FE
|
B:HEM501
|
0.0
|
20.4
|
1.0
|
NC
|
B:HEM501
|
2.0
|
25.8
|
1.0
|
ND
|
B:HEM501
|
2.0
|
24.1
|
1.0
|
NB
|
B:HEM501
|
2.1
|
24.3
|
1.0
|
NA
|
B:HEM501
|
2.2
|
19.0
|
1.0
|
SG
|
B:CYS184
|
2.4
|
16.6
|
1.0
|
C4C
|
B:HEM501
|
3.0
|
14.5
|
1.0
|
C1D
|
B:HEM501
|
3.0
|
18.9
|
1.0
|
C1B
|
B:HEM501
|
3.0
|
25.6
|
1.0
|
C1C
|
B:HEM501
|
3.1
|
24.9
|
1.0
|
C4B
|
B:HEM501
|
3.1
|
25.8
|
1.0
|
C4D
|
B:HEM501
|
3.1
|
24.0
|
1.0
|
C4A
|
B:HEM501
|
3.1
|
26.7
|
1.0
|
C1A
|
B:HEM501
|
3.2
|
16.4
|
1.0
|
CHD
|
B:HEM501
|
3.3
|
16.0
|
1.0
|
CHB
|
B:HEM501
|
3.4
|
25.7
|
1.0
|
CB
|
B:CYS184
|
3.5
|
15.4
|
1.0
|
CHC
|
B:HEM501
|
3.5
|
19.9
|
1.0
|
CHA
|
B:HEM501
|
3.5
|
21.8
|
1.0
|
C05
|
B:V80503
|
4.1
|
15.2
|
1.0
|
CA
|
B:CYS184
|
4.1
|
19.8
|
1.0
|
C04
|
B:V80503
|
4.1
|
17.3
|
1.0
|
C3C
|
B:HEM501
|
4.2
|
19.4
|
1.0
|
C2D
|
B:HEM501
|
4.2
|
19.9
|
1.0
|
C06
|
B:V80503
|
4.2
|
28.4
|
1.0
|
C2B
|
B:HEM501
|
4.3
|
28.9
|
1.0
|
C3D
|
B:HEM501
|
4.3
|
31.8
|
1.0
|
C2C
|
B:HEM501
|
4.3
|
21.6
|
1.0
|
C3B
|
B:HEM501
|
4.3
|
22.6
|
1.0
|
N03
|
B:V80503
|
4.3
|
18.3
|
1.0
|
NE1
|
B:TRP178
|
4.3
|
21.2
|
1.0
|
C3A
|
B:HEM501
|
4.4
|
26.1
|
1.0
|
C2A
|
B:HEM501
|
4.4
|
29.5
|
1.0
|
N01
|
B:V80503
|
4.4
|
27.9
|
1.0
|
C02
|
B:V80503
|
4.4
|
20.5
|
1.0
|
C07
|
B:V80503
|
4.7
|
16.0
|
1.0
|
N
|
B:GLY186
|
4.8
|
24.8
|
1.0
|
C
|
B:CYS184
|
4.9
|
19.2
|
1.0
|
C08
|
B:V80503
|
4.9
|
24.3
|
1.0
|
N
|
B:VAL185
|
5.0
|
20.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 8fgq
Go back to
Iron Binding Sites List in 8fgq
Iron binding site 3 out
of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine
![](/pictures/FE/pdb/fg/8fgq-FE-sphere_03.jpg) Mono view
![](/pictures/FE/pdb/fg/8fgq-FE-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:30.0
occ:1.00
|
FE
|
C:HEM501
|
0.0
|
30.0
|
1.0
|
ND
|
C:HEM501
|
2.1
|
37.8
|
1.0
|
NC
|
C:HEM501
|
2.1
|
43.0
|
1.0
|
NB
|
C:HEM501
|
2.1
|
38.1
|
1.0
|
NA
|
C:HEM501
|
2.1
|
37.1
|
1.0
|
SG
|
C:CYS184
|
2.3
|
28.1
|
1.0
|
C4D
|
C:HEM501
|
3.1
|
42.1
|
1.0
|
C1D
|
C:HEM501
|
3.1
|
41.3
|
1.0
|
C1C
|
C:HEM501
|
3.1
|
42.1
|
1.0
|
C4C
|
C:HEM501
|
3.1
|
36.7
|
1.0
|
C4B
|
C:HEM501
|
3.1
|
39.8
|
1.0
|
C1B
|
C:HEM501
|
3.1
|
44.2
|
1.0
|
C4A
|
C:HEM501
|
3.1
|
37.5
|
1.0
|
C1A
|
C:HEM501
|
3.1
|
40.8
|
1.0
|
CB
|
C:CYS184
|
3.3
|
30.9
|
1.0
|
CHC
|
C:HEM501
|
3.4
|
34.6
|
1.0
|
CHD
|
C:HEM501
|
3.4
|
34.6
|
1.0
|
CHA
|
C:HEM501
|
3.5
|
40.6
|
1.0
|
CHB
|
C:HEM501
|
3.5
|
37.3
|
1.0
|
CA
|
C:CYS184
|
4.1
|
26.8
|
1.0
|
C05
|
C:V80503
|
4.1
|
49.1
|
1.0
|
C04
|
C:V80503
|
4.1
|
51.2
|
1.0
|
N03
|
C:V80503
|
4.3
|
48.9
|
1.0
|
C06
|
C:V80503
|
4.3
|
52.8
|
1.0
|
C2B
|
C:HEM501
|
4.3
|
44.6
|
1.0
|
C3B
|
C:HEM501
|
4.3
|
44.5
|
1.0
|
C3D
|
C:HEM501
|
4.3
|
40.8
|
1.0
|
C2D
|
C:HEM501
|
4.3
|
33.8
|
1.0
|
C2C
|
C:HEM501
|
4.3
|
45.1
|
1.0
|
C3C
|
C:HEM501
|
4.3
|
41.8
|
1.0
|
C3A
|
C:HEM501
|
4.3
|
46.3
|
1.0
|
C2A
|
C:HEM501
|
4.4
|
47.1
|
1.0
|
NE1
|
C:TRP178
|
4.4
|
31.0
|
1.0
|
N01
|
C:V80503
|
4.5
|
49.8
|
1.0
|
C02
|
C:V80503
|
4.5
|
53.6
|
1.0
|
C07
|
C:V80503
|
4.6
|
53.9
|
1.0
|
N
|
C:GLY186
|
4.8
|
30.7
|
1.0
|
C
|
C:CYS184
|
4.8
|
20.3
|
1.0
|
CD1
|
C:TRP178
|
5.0
|
31.6
|
1.0
|
C08
|
C:V80503
|
5.0
|
61.3
|
1.0
|
|
Iron binding site 4 out
of 4 in 8fgq
Go back to
Iron Binding Sites List in 8fgq
Iron binding site 4 out
of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine
![](/pictures/FE/pdb/fg/8fgq-FE-sphere_04.jpg) Mono view
![](/pictures/FE/pdb/fg/8fgq-FE-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:20.9
occ:1.00
|
FE
|
D:HEM501
|
0.0
|
20.9
|
1.0
|
ND
|
D:HEM501
|
2.1
|
19.3
|
1.0
|
NA
|
D:HEM501
|
2.1
|
25.9
|
1.0
|
NC
|
D:HEM501
|
2.1
|
19.4
|
1.0
|
NB
|
D:HEM501
|
2.1
|
23.3
|
1.0
|
SG
|
D:CYS184
|
2.3
|
17.2
|
1.0
|
C4A
|
D:HEM501
|
3.0
|
25.1
|
1.0
|
C1D
|
D:HEM501
|
3.0
|
21.1
|
1.0
|
C1B
|
D:HEM501
|
3.1
|
22.9
|
1.0
|
C4C
|
D:HEM501
|
3.1
|
19.3
|
1.0
|
C4D
|
D:HEM501
|
3.1
|
23.1
|
1.0
|
C1A
|
D:HEM501
|
3.1
|
24.1
|
1.0
|
C1C
|
D:HEM501
|
3.1
|
21.4
|
1.0
|
C4B
|
D:HEM501
|
3.1
|
19.5
|
1.0
|
CB
|
D:CYS184
|
3.4
|
21.1
|
1.0
|
CHB
|
D:HEM501
|
3.4
|
17.6
|
1.0
|
CHD
|
D:HEM501
|
3.4
|
21.1
|
1.0
|
CHA
|
D:HEM501
|
3.5
|
16.8
|
1.0
|
CHC
|
D:HEM501
|
3.5
|
24.6
|
1.0
|
C05
|
D:V80503
|
3.9
|
24.7
|
1.0
|
C04
|
D:V80503
|
4.0
|
25.5
|
1.0
|
CA
|
D:CYS184
|
4.1
|
17.1
|
1.0
|
C06
|
D:V80503
|
4.2
|
32.4
|
1.0
|
N03
|
D:V80503
|
4.3
|
22.6
|
1.0
|
C2D
|
D:HEM501
|
4.3
|
25.7
|
1.0
|
C3A
|
D:HEM501
|
4.3
|
26.6
|
1.0
|
C3D
|
D:HEM501
|
4.3
|
30.3
|
1.0
|
C2B
|
D:HEM501
|
4.3
|
24.7
|
1.0
|
C3C
|
D:HEM501
|
4.3
|
23.2
|
1.0
|
C2A
|
D:HEM501
|
4.3
|
28.1
|
1.0
|
C3B
|
D:HEM501
|
4.3
|
26.4
|
1.0
|
C2C
|
D:HEM501
|
4.3
|
24.6
|
1.0
|
NE1
|
D:TRP178
|
4.4
|
23.6
|
1.0
|
C07
|
D:V80503
|
4.5
|
25.4
|
1.0
|
C02
|
D:V80503
|
4.5
|
21.2
|
1.0
|
N01
|
D:V80503
|
4.5
|
22.7
|
1.0
|
N
|
D:GLY186
|
4.8
|
20.1
|
1.0
|
C
|
D:CYS184
|
4.8
|
16.3
|
1.0
|
N
|
D:VAL185
|
4.9
|
21.9
|
1.0
|
C08
|
D:V80503
|
4.9
|
28.5
|
1.0
|
CD1
|
D:TRP178
|
5.0
|
15.7
|
1.0
|
|
Reference:
D.Vasu,
H.T.Do,
H.Li,
C.D.Hardy,
A.Awasthi,
T.L.Poulos,
R.B.Silverman.
Potent, Selective, and Membrane Permeable 2-Amino-4-Substituted Pyridine-Based Neuronal Nitric Oxide Synthase Inhibitors. J.Med.Chem. V. 66 9934 2023.
ISSN: ISSN 0022-2623
PubMed: 37433128
DOI: 10.1021/ACS.JMEDCHEM.3C00782
Page generated: Sat Aug 10 03:52:01 2024
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