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Gadolinium in PDB 5uoc: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-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 (S)-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 (S)-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 (S)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile, PDB code: 5uoc 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) 39.06 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.961, 153.504, 109.734, 90.00, 90.62, 90.00
R / Rfree (%) 21.2 / 28.8

Other elements in 5uoc:

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

Zinc (Zn) 4 atoms
Iron (Fe) 4 atoms
Chlorine (Cl) 4 atoms

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile (pdb code 5uoc). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 4 binding sites of Gadolinium where determined in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile, PDB code: 5uoc:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 5uoc

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


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-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:Gd510

b:0.4
occ:1.00
O3 A:BTB504 2.6 33.8 1.0
O A:HOH601 2.7 99.0 1.0
O8 A:BTB504 2.7 96.8 1.0
O A:HOH606 2.7 0.5 1.0
O A:HOH607 2.7 0.7 1.0
O A:HOH610 2.8 0.8 1.0
O4 A:BTB504 3.3 89.5 1.0
OD1 A:ASP384 3.6 0.7 1.0
C3 A:BTB504 3.8 66.6 1.0
C4 A:BTB504 3.9 89.0 1.0
N A:BTB504 4.0 98.2 1.0
OD2 A:ASP384 4.1 92.3 1.0
C8 A:BTB504 4.1 99.0 1.0
C2 A:BTB504 4.1 89.1 1.0
CG A:ASP384 4.2 91.9 1.0
O6 A:BTB504 4.5 0.1 1.0
C7 A:BTB504 4.6 97.4 1.0

Gadolinium binding site 2 out of 4 in 5uoc

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


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-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:Gd508

b:69.2
occ:1.00
O3 B:BTB504 2.4 35.2 1.0
O B:HOH601 2.6 58.9 1.0
O6 B:BTB504 2.7 80.5 1.0
O4 B:BTB504 2.7 46.9 1.0
O B:THR319 2.7 84.1 1.0
O B:HOH608 2.7 74.9 1.0
OE1 B:GLU321 2.8 89.3 1.0
O8 B:BTB504 2.8 75.1 1.0
N B:BTB504 2.8 79.9 1.0
C6 B:BTB504 3.4 84.3 1.0
C3 B:BTB504 3.4 63.2 1.0
C8 B:BTB504 3.4 62.4 1.0
C2 B:BTB504 3.5 81.6 1.0
C4 B:BTB504 3.5 72.1 1.0
C5 B:BTB504 3.5 82.3 1.0
C7 B:BTB504 3.7 68.0 1.0
C B:THR319 3.7 74.8 1.0
CD B:GLU321 3.9 87.2 1.0
OD2 C:ASP378 4.3 82.8 1.0
OD1 C:ASP378 4.4 65.3 1.0
OE2 B:GLU321 4.5 87.2 1.0
CA B:THR319 4.5 64.4 1.0
N B:GLU321 4.5 56.3 1.0
N B:LEU320 4.5 78.0 1.0
CA B:LEU320 4.6 60.7 1.0
CB B:THR319 4.6 59.9 1.0
CG C:ASP378 4.8 67.3 1.0
C1 B:BTB504 4.9 93.7 1.0

Gadolinium binding site 3 out of 4 in 5uoc

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


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-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:Gd510

b:0.3
occ:1.00
O3 C:BTB504 2.7 61.5 1.0
O C:HOH604 2.7 0.9 1.0
O6 C:BTB504 2.8 0.4 1.0
O C:HOH608 2.8 0.9 1.0
O C:HOH607 2.8 0.0 1.0
O4 C:BTB504 2.8 0.1 1.0
O8 C:BTB504 2.8 0.8 1.0
N C:BTB504 3.0 0.8 1.0
C6 C:BTB504 3.0 0.2 1.0
C5 C:BTB504 3.3 0.0 1.0
C3 C:BTB504 3.5 82.8 1.0
C2 C:BTB504 3.6 0.1 1.0
C4 C:BTB504 3.7 0.2 1.0
OD1 C:ASP384 3.8 0.2 1.0
C8 C:BTB504 4.0 0.1 1.0
C7 C:BTB504 4.0 0.1 1.0
CG C:ASP384 4.9 0.7 1.0

Gadolinium binding site 4 out of 4 in 5uoc

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


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-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:Gd506

b:65.7
occ:1.00
O D:HOH603 2.3 35.1 1.0
O3 D:BTB504 2.6 49.9 1.0
O4 D:BTB504 2.6 48.4 1.0
OE1 D:GLU321 2.7 74.8 1.0
O D:THR319 2.7 49.9 1.0
OE2 D:GLU321 2.7 87.5 1.0
O6 D:BTB504 2.7 80.7 1.0
O8 D:BTB504 2.8 56.7 1.0
N D:BTB504 3.0 79.3 1.0
C8 D:BTB504 3.0 49.5 1.0
CD D:GLU321 3.0 80.8 1.0
C7 D:BTB504 3.4 66.3 1.0
C4 D:BTB504 3.6 62.1 1.0
C2 D:BTB504 3.7 72.6 1.0
C D:THR319 3.7 63.5 1.0
C3 D:BTB504 3.7 67.5 1.0
C6 D:BTB504 3.7 88.9 1.0
C5 D:BTB504 3.9 86.5 1.0
CA D:THR319 4.4 61.2 1.0
CG D:GLU321 4.5 54.0 1.0
CB D:THR319 4.6 55.0 1.0
N D:LEU320 4.6 59.5 1.0
N D:GLU321 4.7 60.3 1.0
CA D:LEU320 4.7 54.6 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: Sun Dec 13 19:00:17 2020

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