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Fluorine in PDB 3nly: Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine

Enzymatic activity of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine

All present enzymatic activity of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine, PDB code: 3nly was solved by H.Li, S.L.Delker, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.64 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.790, 111.215, 164.089, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.9

Other elements in 3nly:

The structure of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine (pdb code 3nly). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine, PDB code: 3nly:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3nly

Go back to Fluorine Binding Sites List in 3nly
Fluorine binding site 1 out of 6 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F800

b:47.2
occ:1.00
 F5 A:3XC800 0.0 47.2 1.0
C4 A:3XC800 1.3 46.9 1.0
F6 A:3XC800 2.1 50.7 1.0
C3 A:3XC800 2.4 41.8 1.0
C11 A:3XC800 2.4 47.0 1.0
N2 A:3XC800 2.7 38.1 1.0
O A:HOH1058 2.8 43.4 1.0
C12 A:3XC800 2.9 46.9 1.0
CHA A:HEM750 3.3 41.6 1.0
C4D A:HEM750 3.5 40.6 1.0
C1A A:HEM750 3.5 40.1 1.0
C16 A:3XC800 3.7 46.2 1.0
CG2 A:VAL567 3.7 35.5 1.0
CBD A:HEM750 3.8 39.9 1.0
CBA A:HEM750 3.8 47.3 1.0
C2 A:3XC800 3.9 41.5 1.0
O2A A:HEM750 4.0 45.3 1.0
NA A:HEM750 4.0 42.2 1.0
ND A:HEM750 4.0 36.7 1.0
C3D A:HEM750 4.1 39.0 1.0
C2A A:HEM750 4.2 41.4 1.0
C13 A:3XC800 4.3 49.1 1.0
CGA A:HEM750 4.3 48.2 1.0
CAD A:HEM750 4.6 40.7 1.0
CAA A:HEM750 4.7 44.6 1.0
O2D A:HEM750 4.8 41.6 1.0
C4A A:HEM750 4.8 41.2 1.0
C1D A:HEM750 4.8 37.3 1.0
OE1 A:GLU592 4.8 46.0 1.0
FE A:HEM750 4.8 37.1 1.0
C15 A:3XC800 4.8 45.8 1.0
CGD A:HEM750 4.8 42.8 1.0
C3A A:HEM750 4.9 40.2 1.0
C2D A:HEM750 4.9 38.1 1.0
CB A:VAL567 4.9 37.8 1.0

Fluorine binding site 2 out of 6 in 3nly

Go back to Fluorine Binding Sites List in 3nly
Fluorine binding site 2 out of 6 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F800

b:50.7
occ:1.00
 F6 A:3XC800 0.0 50.7 1.0
C4 A:3XC800 1.3 46.9 1.0
F5 A:3XC800 2.1 47.2 1.0
C11 A:3XC800 2.3 47.0 1.0
C3 A:3XC800 2.3 41.8 1.0
C16 A:3XC800 2.7 46.2 1.0
N2 A:3XC800 2.8 38.1 1.0
OE1 A:GLU592 2.9 46.0 1.0
C2A A:HEM750 3.0 41.4 1.0
CBA A:HEM750 3.0 47.3 1.0
C1A A:HEM750 3.1 40.1 1.0
O2A A:HEM750 3.2 45.3 1.0
CGA A:HEM750 3.2 48.2 1.0
C3A A:HEM750 3.3 40.2 1.0
NA A:HEM750 3.4 42.2 1.0
C12 A:3XC800 3.5 46.9 1.0
CAA A:HEM750 3.5 44.6 1.0
CHA A:HEM750 3.6 41.6 1.0
C4A A:HEM750 3.6 41.2 1.0
O A:HOH1019 3.7 39.5 1.0
CD A:GLU592 3.9 45.5 1.0
C15 A:3XC800 4.0 45.8 1.0
O1A A:HEM750 4.1 52.3 1.0
CMA A:HEM750 4.2 36.6 1.0
C2 A:3XC800 4.3 41.5 1.0
O A:HOH1058 4.3 43.4 1.0
C4D A:HEM750 4.4 40.6 1.0
CHB A:HEM750 4.5 36.7 1.0
OE2 A:GLU592 4.5 42.5 1.0
C13 A:3XC800 4.6 49.1 1.0
C14 A:3XC800 4.8 49.1 1.0
ND A:HEM750 4.9 36.7 1.0
CG A:GLU592 4.9 43.1 1.0
FE A:HEM750 5.0 37.1 1.0

Fluorine binding site 3 out of 6 in 3nly

Go back to Fluorine Binding Sites List in 3nly
Fluorine binding site 3 out of 6 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F800

b:51.3
occ:1.00
 F14 A:3XC800 0.0 51.3 1.0
C14 A:3XC800 1.4 49.1 1.0
C15 A:3XC800 2.4 45.8 1.0
C13 A:3XC800 2.4 49.1 1.0
N A:GLY586 2.9 37.5 1.0
N A:TRP587 2.9 39.3 1.0
CA A:GLY586 3.0 37.8 1.0
C4B A:HEM750 3.1 41.3 1.0
CHC A:HEM750 3.2 40.8 1.0
C A:GLY586 3.3 39.4 1.0
O A:TRP587 3.3 38.7 1.0
C3B A:HEM750 3.4 42.4 1.0
C16 A:3XC800 3.6 46.2 1.0
C12 A:3XC800 3.7 46.9 1.0
NB A:HEM750 3.8 39.5 1.0
CG A:PRO565 3.8 39.7 1.0
CAB A:HEM750 3.8 44.9 1.0
C A:TRP587 3.8 40.0 1.0
CA A:TRP587 3.9 40.6 1.0
C A:SER585 4.0 36.6 1.0
C1C A:HEM750 4.0 37.8 1.0
C2B A:HEM750 4.0 42.2 1.0
C11 A:3XC800 4.1 47.0 1.0
O A:PRO565 4.2 38.5 1.0
C1B A:HEM750 4.2 41.5 1.0
CBB A:HEM750 4.2 44.6 1.0
O A:GLY586 4.3 40.0 1.0
CB A:PRO565 4.4 38.6 1.0
CA A:SER585 4.7 35.4 1.0
NC A:HEM750 4.7 37.9 1.0
O A:SER585 4.8 36.6 1.0
CD A:PRO565 4.8 41.0 1.0
C2C A:HEM750 4.9 39.9 1.0
N A:TYR588 4.9 41.3 1.0

Fluorine binding site 4 out of 6 in 3nly

Go back to Fluorine Binding Sites List in 3nly
Fluorine binding site 4 out of 6 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F800

b:45.8
occ:1.00
 F5 B:3XC800 0.0 45.8 1.0
C4 B:3XC800 1.3 46.5 1.0
F6 B:3XC800 2.1 50.6 1.0
C3 B:3XC800 2.4 43.7 1.0
C11 B:3XC800 2.4 45.3 1.0
O B:HOH1048 2.8 42.1 1.0
N2 B:3XC800 2.8 39.0 1.0
C12 B:3XC800 2.8 44.6 1.0
CHA B:HEM750 3.5 37.4 1.0
CG2 B:VAL567 3.6 34.6 1.0
C16 B:3XC800 3.7 43.5 1.0
C4D B:HEM750 3.7 36.0 1.0
CBD B:HEM750 3.7 39.8 1.0
C1A B:HEM750 3.8 40.6 1.0
CBA B:HEM750 3.9 49.3 1.0
O2A B:HEM750 4.0 51.1 1.0
C2 B:3XC800 4.1 44.0 1.0
ND B:HEM750 4.1 33.6 1.0
C3D B:HEM750 4.2 37.2 1.0
C13 B:3XC800 4.2 45.2 1.0
C2A B:HEM750 4.3 42.2 1.0
CGA B:HEM750 4.3 49.9 1.0
NA B:HEM750 4.3 39.3 1.0
CAD B:HEM750 4.6 37.7 1.0
O2D B:HEM750 4.6 45.6 1.0
CAA B:HEM750 4.7 45.0 1.0
CGD B:HEM750 4.7 41.5 1.0
C15 B:3XC800 4.8 44.1 1.0
CB B:VAL567 4.8 34.9 1.0
C1D B:HEM750 4.8 34.4 1.0
FE B:HEM750 4.8 35.9 1.0
C2D B:HEM750 4.9 36.0 1.0
C3A B:HEM750 5.0 40.0 1.0
C4A B:HEM750 5.0 39.6 1.0
C14 B:3XC800 5.0 46.9 1.0

Fluorine binding site 5 out of 6 in 3nly

Go back to Fluorine Binding Sites List in 3nly
Fluorine binding site 5 out of 6 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F800

b:50.6
occ:1.00
 F6 B:3XC800 0.0 50.6 1.0
C4 B:3XC800 1.3 46.5 1.0
F5 B:3XC800 2.1 45.8 1.0
C11 B:3XC800 2.3 45.3 1.0
C3 B:3XC800 2.4 43.7 1.0
C16 B:3XC800 2.8 43.5 1.0
C2A B:HEM750 2.9 42.2 1.0
CBA B:HEM750 2.9 49.3 1.0
N2 B:3XC800 3.0 39.0 1.0
CGA B:HEM750 3.0 49.9 1.0
O2A B:HEM750 3.0 51.1 1.0
C1A B:HEM750 3.1 40.6 1.0
C3A B:HEM750 3.3 40.0 1.0
OE1 B:GLU592 3.3 44.5 1.0
CAA B:HEM750 3.3 45.0 1.0
C12 B:3XC800 3.6 44.6 1.0
NA B:HEM750 3.6 39.3 1.0
CHA B:HEM750 3.6 37.4 1.0
O1A B:HEM750 3.7 53.8 1.0
C4A B:HEM750 3.7 39.6 1.0
O B:HOH1006 3.9 37.7 1.0
CMA B:HEM750 4.1 38.1 1.0
C15 B:3XC800 4.2 44.1 1.0
CD B:GLU592 4.2 45.3 1.0
O B:HOH1048 4.2 42.1 1.0
C4D B:HEM750 4.4 36.0 1.0
C2 B:3XC800 4.4 44.0 1.0
OE2 B:GLU592 4.7 41.6 1.0
CHB B:HEM750 4.7 38.9 1.0
C13 B:3XC800 4.7 45.2 1.0
FE B:HEM750 4.9 35.9 1.0
ND B:HEM750 4.9 33.6 1.0
C14 B:3XC800 4.9 46.9 1.0

Fluorine binding site 6 out of 6 in 3nly

Go back to Fluorine Binding Sites List in 3nly
Fluorine binding site 6 out of 6 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(4-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F800

b:51.2
occ:1.00
 F14 B:3XC800 0.0 51.2 1.0
C14 B:3XC800 1.3 46.9 1.0
C13 B:3XC800 2.4 45.2 1.0
C15 B:3XC800 2.4 44.1 1.0
N B:GLY586 2.7 35.2 1.0
CA B:GLY586 3.0 36.1 1.0
N B:TRP587 3.2 36.8 1.0
C4B B:HEM750 3.2 40.5 1.0
CHC B:HEM750 3.3 36.2 1.0
C B:GLY586 3.3 37.2 1.0
C3B B:HEM750 3.5 41.3 1.0
C12 B:3XC800 3.6 44.6 1.0
O B:TRP587 3.6 35.9 1.0
C16 B:3XC800 3.6 43.5 1.0
CG B:PRO565 3.8 35.5 1.0
C B:SER585 3.8 34.6 1.0
NB B:HEM750 3.8 37.0 1.0
CAB B:HEM750 3.9 43.0 1.0
C1C B:HEM750 4.0 35.5 1.0
O B:PRO565 4.1 35.2 1.0
C11 B:3XC800 4.1 45.3 1.0
C B:TRP587 4.1 36.5 1.0
CA B:TRP587 4.2 37.5 1.0
C2B B:HEM750 4.2 40.2 1.0
O B:GLY586 4.3 37.2 1.0
C1B B:HEM750 4.3 39.1 1.0
CBB B:HEM750 4.4 45.7 1.0
CA B:SER585 4.4 33.2 1.0
CB B:PRO565 4.5 34.9 1.0
O B:SER585 4.6 32.3 1.0
NC B:HEM750 4.6 34.5 1.0
C2C B:HEM750 4.7 36.1 1.0
CD B:PRO565 4.7 38.2 1.0
C B:PRO565 5.0 35.8 1.0
CMC B:HEM750 5.0 33.8 1.0

Reference:

F.Xue, H.Li, S.L.Delker, J.Fang, P.Martasek, L.J.Roman, T.L.Poulos, R.B.Silverman. Potent, Highly Selective, and Orally Bioavailable Gem-Difluorinated Monocationic Inhibitors of Neuronal Nitric Oxide Synthase. J.Am.Chem.Soc. V. 132 14229 2010.
ISSN: ISSN 0002-7863
PubMed: 20843082
DOI: 10.1021/JA106175Q
Page generated: Mon Jul 14 18:07:37 2025

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