Iron in PDB 5vvc: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile
Enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile
All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile:
1.14.13.39;
Protein crystallography data
The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile, PDB code: 5vvc
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)
|
88.56 /
2.40
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
59.330,
152.620,
108.740,
90.00,
90.57,
90.00
|
R / Rfree (%)
|
20.6 /
27.2
|
Other elements in 5vvc:
The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile 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-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile
(pdb code 5vvc). 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-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile, PDB code: 5vvc:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 5vvc
Go back to
Iron Binding Sites List in 5vvc
Iron binding site 1 out
of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile
Mono view
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-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:57.0
occ:1.00
|
FE
|
A:HEM501
|
0.0
|
57.0
|
1.0
|
NB
|
A:HEM501
|
2.0
|
51.9
|
1.0
|
NC
|
A:HEM501
|
2.0
|
59.5
|
1.0
|
NA
|
A:HEM501
|
2.1
|
45.2
|
1.0
|
ND
|
A:HEM501
|
2.1
|
52.2
|
1.0
|
SG
|
A:CYS184
|
2.3
|
51.1
|
1.0
|
C1B
|
A:HEM501
|
3.0
|
50.5
|
1.0
|
C4A
|
A:HEM501
|
3.0
|
48.7
|
1.0
|
C4C
|
A:HEM501
|
3.0
|
58.8
|
1.0
|
C1D
|
A:HEM501
|
3.1
|
58.5
|
1.0
|
C1C
|
A:HEM501
|
3.1
|
56.4
|
1.0
|
C4B
|
A:HEM501
|
3.1
|
52.6
|
1.0
|
C4D
|
A:HEM501
|
3.1
|
51.4
|
1.0
|
C1A
|
A:HEM501
|
3.1
|
46.2
|
1.0
|
CB
|
A:CYS184
|
3.3
|
50.0
|
1.0
|
CHB
|
A:HEM501
|
3.3
|
49.2
|
1.0
|
CHD
|
A:HEM501
|
3.4
|
60.1
|
1.0
|
CHC
|
A:HEM501
|
3.5
|
53.2
|
1.0
|
CHA
|
A:HEM501
|
3.5
|
48.3
|
1.0
|
C13
|
A:9OJ503
|
3.8
|
43.8
|
1.0
|
C14
|
A:9OJ503
|
3.8
|
47.3
|
1.0
|
C15
|
A:9OJ503
|
3.9
|
39.2
|
1.0
|
CA
|
A:CYS184
|
4.2
|
47.3
|
1.0
|
C2B
|
A:HEM501
|
4.2
|
47.4
|
1.0
|
C3C
|
A:HEM501
|
4.3
|
55.1
|
1.0
|
C3A
|
A:HEM501
|
4.3
|
47.6
|
1.0
|
C3B
|
A:HEM501
|
4.3
|
51.0
|
1.0
|
C2C
|
A:HEM501
|
4.3
|
58.1
|
1.0
|
C2D
|
A:HEM501
|
4.3
|
59.5
|
1.0
|
C3D
|
A:HEM501
|
4.3
|
54.6
|
1.0
|
C2A
|
A:HEM501
|
4.3
|
47.5
|
1.0
|
NE1
|
A:TRP178
|
4.4
|
56.4
|
1.0
|
C12
|
A:9OJ503
|
4.5
|
46.3
|
1.0
|
C16
|
A:9OJ503
|
4.6
|
42.9
|
1.0
|
N
|
A:GLY186
|
4.8
|
46.6
|
1.0
|
C
|
A:CYS184
|
4.9
|
46.7
|
1.0
|
N
|
A:VAL185
|
5.0
|
42.9
|
1.0
|
|
Iron binding site 2 out
of 4 in 5vvc
Go back to
Iron Binding Sites List in 5vvc
Iron binding site 2 out
of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile
Mono view
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-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:31.2
occ:1.00
|
FE
|
B:HEM501
|
0.0
|
31.2
|
1.0
|
NA
|
B:HEM501
|
2.1
|
43.4
|
1.0
|
ND
|
B:HEM501
|
2.1
|
45.5
|
1.0
|
NB
|
B:HEM501
|
2.1
|
43.5
|
1.0
|
NC
|
B:HEM501
|
2.1
|
49.6
|
1.0
|
SG
|
B:CYS184
|
2.2
|
30.1
|
1.0
|
C4A
|
B:HEM501
|
3.0
|
40.6
|
1.0
|
C1D
|
B:HEM501
|
3.0
|
44.7
|
1.0
|
C4C
|
B:HEM501
|
3.1
|
48.4
|
1.0
|
C1B
|
B:HEM501
|
3.1
|
44.3
|
1.0
|
C1A
|
B:HEM501
|
3.1
|
42.0
|
1.0
|
C4D
|
B:HEM501
|
3.1
|
47.1
|
1.0
|
C4B
|
B:HEM501
|
3.2
|
45.8
|
1.0
|
C1C
|
B:HEM501
|
3.2
|
49.2
|
1.0
|
CB
|
B:CYS184
|
3.3
|
45.5
|
1.0
|
CHD
|
B:HEM501
|
3.3
|
45.4
|
1.0
|
CHB
|
B:HEM501
|
3.3
|
40.3
|
1.0
|
CHA
|
B:HEM501
|
3.5
|
43.8
|
1.0
|
CHC
|
B:HEM501
|
3.6
|
48.9
|
1.0
|
C13
|
B:9OJ503
|
3.7
|
49.1
|
1.0
|
C14
|
B:9OJ503
|
3.7
|
53.7
|
1.0
|
C15
|
B:9OJ503
|
3.8
|
46.5
|
1.0
|
CA
|
B:CYS184
|
4.0
|
42.1
|
1.0
|
C3A
|
B:HEM501
|
4.3
|
39.9
|
1.0
|
C2D
|
B:HEM501
|
4.3
|
44.5
|
1.0
|
C2A
|
B:HEM501
|
4.3
|
39.9
|
1.0
|
NE1
|
B:TRP178
|
4.3
|
37.0
|
1.0
|
C2B
|
B:HEM501
|
4.3
|
45.9
|
1.0
|
C3D
|
B:HEM501
|
4.3
|
44.7
|
1.0
|
C3C
|
B:HEM501
|
4.3
|
51.2
|
1.0
|
C3B
|
B:HEM501
|
4.4
|
46.2
|
1.0
|
C2C
|
B:HEM501
|
4.4
|
51.9
|
1.0
|
C12
|
B:9OJ503
|
4.4
|
45.0
|
1.0
|
C16
|
B:9OJ503
|
4.5
|
41.7
|
1.0
|
C
|
B:CYS184
|
4.8
|
41.3
|
1.0
|
N
|
B:GLY186
|
4.9
|
39.4
|
1.0
|
N
|
B:VAL185
|
5.0
|
44.1
|
1.0
|
C11
|
B:9OJ503
|
5.0
|
39.7
|
1.0
|
|
Iron binding site 3 out
of 4 in 5vvc
Go back to
Iron Binding Sites List in 5vvc
Iron binding site 3 out
of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile
Mono view
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-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:44.1
occ:1.00
|
FE
|
C:HEM501
|
0.0
|
44.1
|
1.0
|
NC
|
C:HEM501
|
2.0
|
54.0
|
1.0
|
NA
|
C:HEM501
|
2.1
|
33.9
|
1.0
|
ND
|
C:HEM501
|
2.1
|
47.3
|
1.0
|
NB
|
C:HEM501
|
2.2
|
46.0
|
1.0
|
SG
|
C:CYS184
|
2.4
|
43.3
|
1.0
|
C4C
|
C:HEM501
|
3.0
|
53.1
|
1.0
|
C1C
|
C:HEM501
|
3.0
|
56.6
|
1.0
|
C1D
|
C:HEM501
|
3.1
|
50.5
|
1.0
|
C1A
|
C:HEM501
|
3.1
|
40.2
|
1.0
|
C4D
|
C:HEM501
|
3.1
|
47.2
|
1.0
|
C4A
|
C:HEM501
|
3.1
|
35.5
|
1.0
|
C4B
|
C:HEM501
|
3.2
|
48.1
|
1.0
|
C1B
|
C:HEM501
|
3.2
|
45.4
|
1.0
|
CB
|
C:CYS184
|
3.3
|
35.7
|
1.0
|
CHD
|
C:HEM501
|
3.4
|
52.4
|
1.0
|
CHA
|
C:HEM501
|
3.5
|
42.3
|
1.0
|
CHC
|
C:HEM501
|
3.5
|
51.2
|
1.0
|
CHB
|
C:HEM501
|
3.5
|
40.6
|
1.0
|
C15
|
C:9OJ503
|
3.8
|
56.1
|
1.0
|
C13
|
C:9OJ503
|
3.9
|
57.2
|
1.0
|
C14
|
C:9OJ503
|
3.9
|
56.2
|
1.0
|
CA
|
C:CYS184
|
4.1
|
38.6
|
1.0
|
C3C
|
C:HEM501
|
4.2
|
53.6
|
1.0
|
C2C
|
C:HEM501
|
4.2
|
57.7
|
1.0
|
C2A
|
C:HEM501
|
4.3
|
38.9
|
1.0
|
C2D
|
C:HEM501
|
4.3
|
47.9
|
1.0
|
C3A
|
C:HEM501
|
4.4
|
35.7
|
1.0
|
C3D
|
C:HEM501
|
4.4
|
49.5
|
1.0
|
C3B
|
C:HEM501
|
4.4
|
49.2
|
1.0
|
C2B
|
C:HEM501
|
4.4
|
45.7
|
1.0
|
NE1
|
C:TRP178
|
4.4
|
49.3
|
1.0
|
C16
|
C:9OJ503
|
4.5
|
53.6
|
1.0
|
C12
|
C:9OJ503
|
4.5
|
58.4
|
1.0
|
N
|
C:GLY186
|
4.6
|
45.3
|
1.0
|
C
|
C:CYS184
|
4.8
|
37.5
|
1.0
|
N
|
C:VAL185
|
4.9
|
37.3
|
1.0
|
CA
|
C:GLY186
|
4.9
|
47.6
|
1.0
|
CD1
|
C:TRP178
|
5.0
|
49.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 5vvc
Go back to
Iron Binding Sites List in 5vvc
Iron binding site 4 out
of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile
Mono view
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-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:33.3
occ:1.00
|
FE
|
D:HEM501
|
0.0
|
33.3
|
1.0
|
NA
|
D:HEM501
|
2.0
|
40.9
|
1.0
|
ND
|
D:HEM501
|
2.1
|
37.7
|
1.0
|
NC
|
D:HEM501
|
2.1
|
37.8
|
1.0
|
NB
|
D:HEM501
|
2.1
|
40.4
|
1.0
|
SG
|
D:CYS184
|
2.2
|
28.7
|
1.0
|
C1D
|
D:HEM501
|
3.0
|
36.7
|
1.0
|
C4A
|
D:HEM501
|
3.0
|
36.4
|
1.0
|
C4C
|
D:HEM501
|
3.0
|
34.3
|
1.0
|
C1A
|
D:HEM501
|
3.1
|
42.3
|
1.0
|
C1B
|
D:HEM501
|
3.1
|
40.2
|
1.0
|
C4D
|
D:HEM501
|
3.1
|
40.2
|
1.0
|
C1C
|
D:HEM501
|
3.2
|
39.0
|
1.0
|
C4B
|
D:HEM501
|
3.2
|
41.0
|
1.0
|
CHD
|
D:HEM501
|
3.3
|
34.1
|
1.0
|
CB
|
D:CYS184
|
3.3
|
41.1
|
1.0
|
CHB
|
D:HEM501
|
3.4
|
36.2
|
1.0
|
CHA
|
D:HEM501
|
3.5
|
43.0
|
1.0
|
C14
|
D:9OJ503
|
3.5
|
49.0
|
1.0
|
CHC
|
D:HEM501
|
3.6
|
41.0
|
1.0
|
C13
|
D:9OJ503
|
3.7
|
46.5
|
1.0
|
C15
|
D:9OJ503
|
3.8
|
41.1
|
1.0
|
CA
|
D:CYS184
|
4.1
|
33.3
|
1.0
|
C3A
|
D:HEM501
|
4.3
|
36.3
|
1.0
|
C2D
|
D:HEM501
|
4.3
|
38.9
|
1.0
|
C2A
|
D:HEM501
|
4.3
|
36.4
|
1.0
|
C3C
|
D:HEM501
|
4.3
|
37.9
|
1.0
|
C3D
|
D:HEM501
|
4.3
|
38.4
|
1.0
|
C2B
|
D:HEM501
|
4.3
|
40.7
|
1.0
|
C2C
|
D:HEM501
|
4.4
|
38.4
|
1.0
|
C3B
|
D:HEM501
|
4.4
|
40.2
|
1.0
|
C12
|
D:9OJ503
|
4.5
|
45.8
|
1.0
|
NE1
|
D:TRP178
|
4.6
|
40.0
|
1.0
|
C16
|
D:9OJ503
|
4.6
|
36.1
|
1.0
|
N
|
D:GLY186
|
4.7
|
39.8
|
1.0
|
C
|
D:CYS184
|
4.8
|
34.8
|
1.0
|
N
|
D:VAL185
|
5.0
|
36.8
|
1.0
|
|
Reference:
A.V.Pensa,
M.A.Cinelli,
H.Li,
G.Chreifi,
P.Mukherjee,
L.J.Roman,
P.Martasek,
T.L.Poulos,
R.B.Silverman.
Hydrophilic, Potent, and Selective 7-Substituted 2-Aminoquinolines As Improved Human Neuronal Nitric Oxide Synthase Inhibitors. J. Med. Chem. V. 60 7146 2017.
ISSN: ISSN 1520-4804
PubMed: 28776992
DOI: 10.1021/ACS.JMEDCHEM.7B00835
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