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Iron in PDB 5uob: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile

Enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile

All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile:
1.14.13.39;

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile, PDB code: 5uob 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) 38.49 / 2.29
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.534, 153.951, 109.828, 90.00, 90.57, 90.00
R / Rfree (%) 22.1 / 27.9

Other elements in 5uob:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile also contains other interesting chemical elements:

Zinc (Zn) 6 atoms
Gadolinium (Gd) 4 atoms
Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile (pdb code 5uob). 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 (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile, PDB code: 5uob:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5uob

Go back to Iron Binding Sites List in 5uob
Iron binding site 1 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile


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 (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:55.8
occ:1.00
 FE A:HEM501 0.0 55.8 1.0
ND A:HEM501 2.1 52.7 1.0
NA A:HEM501 2.1 53.8 1.0
NC A:HEM501 2.1 69.5 1.0
NB A:HEM501 2.1 50.8 1.0
SG A:CYS184 2.4 56.9 1.0
C1D A:HEM501 3.1 60.7 1.0
C1A A:HEM501 3.1 51.8 1.0
C4D A:HEM501 3.1 54.5 1.0
C4C A:HEM501 3.1 68.1 1.0
C1C A:HEM501 3.1 67.8 1.0
C4B A:HEM501 3.1 56.2 1.0
C4A A:HEM501 3.1 55.0 1.0
C1B A:HEM501 3.1 52.1 1.0
CB A:CYS184 3.2 51.7 1.0
CHA A:HEM501 3.4 48.6 1.0
CHD A:HEM501 3.4 63.9 1.0
CHC A:HEM501 3.5 62.3 1.0
CHB A:HEM501 3.5 53.0 1.0
C11 A:M4R502 3.6 0.8 1.0
C04 A:M4R502 3.6 99.5 1.0
C03 A:M4R502 4.0 97.0 1.0
C05 A:M4R502 4.0 0.5 1.0
CA A:CYS184 4.0 51.6 1.0
C2D A:HEM501 4.3 63.4 1.0
C3C A:HEM501 4.3 68.5 1.0
C2A A:HEM501 4.3 54.4 1.0
C3D A:HEM501 4.3 60.4 1.0
C2C A:HEM501 4.3 71.3 1.0
C3A A:HEM501 4.3 54.8 1.0
C2B A:HEM501 4.3 52.5 1.0
C3B A:HEM501 4.3 53.0 1.0
C06 A:M4R502 4.4 0.6 1.0
NE1 A:TRP178 4.6 53.9 1.0
C02 A:M4R502 4.7 95.4 1.0
C10 A:M4R502 4.7 99.7 1.0
C A:CYS184 4.8 51.4 1.0
N A:GLY186 4.8 47.8 1.0
N A:VAL185 4.9 52.8 1.0
N01 A:M4R502 5.0 96.7 1.0

Iron binding site 2 out of 4 in 5uob

Go back to Iron Binding Sites List in 5uob
Iron binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile


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 (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:42.4
occ:1.00
 FE B:HEM501 0.0 42.4 1.0
NA B:HEM501 2.0 45.0 1.0
NC B:HEM501 2.1 51.2 1.0
ND B:HEM501 2.1 44.1 1.0
NB B:HEM501 2.1 45.3 1.0
SG B:CYS184 2.3 39.3 1.0
C4C B:HEM501 3.0 44.1 1.0
C1D B:HEM501 3.0 47.4 1.0
C4A B:HEM501 3.0 40.8 1.0
C1A B:HEM501 3.1 48.3 1.0
C1B B:HEM501 3.1 42.5 1.0
C1C B:HEM501 3.1 53.9 1.0
C4D B:HEM501 3.1 45.5 1.0
C4B B:HEM501 3.1 50.0 1.0
CB B:CYS184 3.2 39.8 1.0
CHD B:HEM501 3.3 43.0 1.0
CHB B:HEM501 3.4 40.5 1.0
CHA B:HEM501 3.5 45.9 1.0
CHC B:HEM501 3.5 51.8 1.0
C05 B:M4R502 3.9 72.1 1.0
C04 B:M4R502 4.0 65.8 1.0
CA B:CYS184 4.0 41.2 1.0
C06 B:M4R502 4.2 74.5 1.0
C11 B:M4R502 4.3 59.3 1.0
C3A B:HEM501 4.3 42.5 1.0
C2A B:HEM501 4.3 40.6 1.0
C3C B:HEM501 4.3 53.5 1.0
C2D B:HEM501 4.3 46.3 1.0
C2B B:HEM501 4.3 46.9 1.0
C2C B:HEM501 4.3 53.1 1.0
C3B B:HEM501 4.3 48.4 1.0
C3D B:HEM501 4.4 44.9 1.0
C10 B:M4R502 4.4 72.5 1.0
C03 B:M4R502 4.4 69.0 1.0
NE1 B:TRP178 4.4 46.8 1.0
C B:CYS184 4.8 41.0 1.0
N01 B:M4R502 4.8 71.9 1.0
C02 B:M4R502 4.8 70.3 1.0
C07 B:M4R502 4.8 78.6 1.0
N B:VAL185 4.8 38.7 1.0
N B:GLY186 4.9 42.7 1.0

Iron binding site 3 out of 4 in 5uob

Go back to Iron Binding Sites List in 5uob
Iron binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile


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 (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:48.5
occ:1.00
 FE C:HEM501 0.0 48.5 1.0
ND C:HEM501 2.1 53.3 1.0
NC C:HEM501 2.1 64.2 1.0
NA C:HEM501 2.1 51.3 1.0
NB C:HEM501 2.2 60.0 1.0
SG C:CYS184 2.2 40.4 1.0
C4C C:HEM501 3.0 60.5 1.0
C1D C:HEM501 3.0 55.8 1.0
C4D C:HEM501 3.1 50.2 1.0
C1A C:HEM501 3.1 51.7 1.0
C1C C:HEM501 3.1 62.2 1.0
CB C:CYS184 3.1 38.2 1.0
C4A C:HEM501 3.1 54.1 1.0
C1B C:HEM501 3.1 58.9 1.0
C4B C:HEM501 3.2 58.2 1.0
CHD C:HEM501 3.4 56.8 1.0
CHA C:HEM501 3.4 45.8 1.0
CHC C:HEM501 3.5 59.6 1.0
CHB C:HEM501 3.5 60.3 1.0
C04 C:M4R502 3.8 0.6 1.0
C05 C:M4R502 4.0 0.3 1.0
CA C:CYS184 4.0 40.6 1.0
C11 C:M4R502 4.1 0.4 1.0
C03 C:M4R502 4.2 0.6 1.0
C3C C:HEM501 4.3 58.0 1.0
C3D C:HEM501 4.3 54.6 1.0
C2D C:HEM501 4.3 53.8 1.0
C2C C:HEM501 4.3 63.1 1.0
NE1 C:TRP178 4.3 40.8 1.0
C2A C:HEM501 4.3 53.7 1.0
C2B C:HEM501 4.3 59.9 1.0
C3A C:HEM501 4.3 49.0 1.0
C3B C:HEM501 4.4 53.8 1.0
C06 C:M4R502 4.4 0.8 1.0
C10 C:M4R502 4.5 0.9 1.0
C02 C:M4R502 4.6 0.7 1.0
N01 C:M4R502 4.7 0.9 1.0
C C:CYS184 4.8 39.8 1.0
N C:GLY186 4.9 43.7 1.0
CD1 C:TRP178 5.0 41.4 1.0

Iron binding site 4 out of 4 in 5uob

Go back to Iron Binding Sites List in 5uob
Iron binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile


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 (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:41.0
occ:1.00
 FE D:HEM501 0.0 41.0 1.0
ND D:HEM501 2.0 53.3 1.0
NA D:HEM501 2.1 57.1 1.0
NC D:HEM501 2.1 53.0 1.0
NB D:HEM501 2.1 56.8 1.0
SG D:CYS184 2.3 38.8 1.0
C1D D:HEM501 3.0 53.2 1.0
C4D D:HEM501 3.0 54.4 1.0
C4C D:HEM501 3.0 50.6 1.0
C1A D:HEM501 3.1 54.0 1.0
C1B D:HEM501 3.1 58.6 1.0
C4A D:HEM501 3.1 54.1 1.0
C4B D:HEM501 3.2 57.7 1.0
C1C D:HEM501 3.2 56.4 1.0
CB D:CYS184 3.3 38.5 1.0
CHD D:HEM501 3.3 51.6 1.0
CHA D:HEM501 3.4 52.1 1.0
CHB D:HEM501 3.5 55.0 1.0
CHC D:HEM501 3.6 58.6 1.0
C04 D:M4R502 3.7 73.6 1.0
C05 D:M4R502 3.9 77.4 1.0
CA D:CYS184 4.1 41.7 1.0
C03 D:M4R502 4.1 70.5 1.0
C11 D:M4R502 4.1 74.3 1.0
C2D D:HEM501 4.2 52.5 1.0
C3D D:HEM501 4.2 52.8 1.0
C06 D:M4R502 4.3 80.3 1.0
C10 D:M4R502 4.3 76.6 1.0
C2A D:HEM501 4.3 49.5 1.0
C3C D:HEM501 4.3 56.0 1.0
C3A D:HEM501 4.3 50.9 1.0
C2B D:HEM501 4.3 61.6 1.0
C3B D:HEM501 4.4 57.7 1.0
C2C D:HEM501 4.4 57.2 1.0
C02 D:M4R502 4.5 71.9 1.0
NE1 D:TRP178 4.5 40.3 1.0
N01 D:M4R502 4.6 76.7 1.0
C D:CYS184 4.9 41.8 1.0
N D:GLY186 4.9 39.6 1.0
C07 D:M4R502 5.0 81.9 1.0

Reference:

M.A.Cinelli, H.Li, G.Chreifi, T.L.Poulos, R.B.Silverman. Nitrile in the Hole: Discovery of A Small Auxiliary Pocket in Neuronal Nitric Oxide Synthase Leading to the Development of Potent and Selective 2-Aminoquinoline Inhibitors. J. Med. Chem. V. 60 3958 2017.
ISSN: ISSN 1520-4804
PubMed: 28422508
DOI: 10.1021/ACS.JMEDCHEM.7B00259
Page generated: Tue Aug 6 09:59:06 2024

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