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Fluorine in PDB 3nlv: Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-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-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-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-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-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-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine, PDB code: 3nlv 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) 41.06 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.266, 111.663, 164.439, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.1

Other elements in 3nlv:

The structure of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-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-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine (pdb code 3nlv). 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-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-Fluorophenyl)Ethylamino) Ethoxy)Pyrrolidin-3-Yl)Methyl)-4-Methylpyridin-2-Amine, PDB code: 3nlv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3nlv

Go back to Fluorine Binding Sites List in 3nlv
Fluorine binding site 1 out of 6 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-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-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-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:58.6
occ:1.00
 F7 A:3XA800 0.0 58.6 1.0
C6 A:3XA800 1.3 57.6 1.0
F8 A:3XA800 2.2 59.3 1.0
C11 A:3XA800 2.3 58.1 1.0
C5 A:3XA800 2.3 53.7 1.0
N4 A:3XA800 2.6 48.5 1.0
C3 A:3XA800 3.0 44.4 1.0
C16 A:3XA800 3.1 59.4 1.0
C12 A:3XA800 3.2 59.1 1.0
C2 A:3XA800 4.0 39.4 1.0
O2D A:HEM750 4.1 37.6 1.0
O A:HOH1005 4.2 26.4 1.0
C15 A:3XA800 4.4 59.4 1.0
C13 A:3XA800 4.4 59.9 1.0
CE2 A:TYR706 4.6 45.2 1.0
C14 A:3XA800 4.9 59.6 1.0

Fluorine binding site 2 out of 6 in 3nlv

Go back to Fluorine Binding Sites List in 3nlv
Fluorine binding site 2 out of 6 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-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-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-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:59.3
occ:1.00
 F8 A:3XA800 0.0 59.3 1.0
C6 A:3XA800 1.3 57.6 1.0
F7 A:3XA800 2.2 58.6 1.0
C5 A:3XA800 2.3 53.7 1.0
C11 A:3XA800 2.3 58.1 1.0
C16 A:3XA800 2.7 59.4 1.0
C3 A:3XA800 3.0 44.4 1.0
N4 A:3XA800 3.0 48.5 1.0
C12 A:3XA800 3.5 59.1 1.0
C15 A:3XA800 4.1 59.4 1.0
O A:HOH1023 4.1 33.6 1.0
C2 A:3XA800 4.4 39.4 1.0
O A:HOH1157 4.5 33.6 1.0
O A:HOH1067 4.6 25.9 1.0
C13 A:3XA800 4.7 59.9 1.0
O A:HOH1101 4.8 47.2 1.0
C14 A:3XA800 4.9 59.6 1.0

Fluorine binding site 3 out of 6 in 3nlv

Go back to Fluorine Binding Sites List in 3nlv
Fluorine binding site 3 out of 6 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-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-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-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:60.7
occ:1.00
 F13 A:3XA800 0.0 60.7 1.0
C13 A:3XA800 1.3 59.9 1.0
C12 A:3XA800 2.4 59.1 1.0
C14 A:3XA800 2.4 59.6 1.0
CD2 A:LEU337 3.2 44.3 1.0
O A:MET336 3.3 35.4 1.0
CB A:MET336 3.4 36.5 1.0
C A:MET336 3.6 36.6 1.0
C11 A:3XA800 3.6 58.1 1.0
C15 A:3XA800 3.7 59.4 1.0
CE A:MET336 3.7 38.7 1.0
OH A:TYR706 3.7 47.2 1.0
CZ A:TYR706 3.7 45.5 1.0
CG A:LEU337 3.8 43.9 1.0
CA A:MET336 4.0 35.5 1.0
CE1 A:TYR706 4.0 47.1 1.0
NH1 A:ARG414 4.1 29.6 1.0
C16 A:3XA800 4.1 59.4 1.0
CE2 A:TYR706 4.2 45.2 1.0
CG A:MET336 4.3 39.7 1.0
N A:LEU337 4.4 39.3 1.0
CZ2 A:TRP678 4.4 31.7 1.0
SD A:MET336 4.5 43.0 1.0
CD1 A:TYR706 4.7 46.6 1.0
CH2 A:TRP678 4.7 32.6 1.0
CD1 A:LEU337 4.7 48.5 1.0
CD2 A:TYR706 4.9 44.5 1.0
C6 A:3XA800 4.9 57.6 1.0
CB A:LEU337 4.9 44.0 1.0
CA A:LEU337 4.9 42.4 1.0
C5 A:3XA800 5.0 53.7 1.0

Fluorine binding site 4 out of 6 in 3nlv

Go back to Fluorine Binding Sites List in 3nlv
Fluorine binding site 4 out of 6 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-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-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-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:55.2
occ:1.00
 F7 B:3XA800 0.0 55.2 1.0
C6 B:3XA800 1.3 56.0 1.0
F8 B:3XA800 2.2 57.6 1.0
C11 B:3XA800 2.3 56.9 1.0
C5 B:3XA800 2.3 53.6 1.0
C12 B:3XA800 2.5 59.2 1.0
N4 B:3XA800 2.7 51.0 1.0
O2D B:HEM750 2.7 32.4 1.0
O B:HOH1197 3.2 42.9 1.0
C16 B:3XA800 3.5 58.0 1.0
C3 B:3XA800 3.6 46.6 1.0
CE2 B:TYR706 3.7 40.4 1.0
CGD B:HEM750 3.9 31.0 1.0
C13 B:3XA800 3.9 60.5 1.0
C2 B:3XA800 4.0 41.8 1.0
OH B:TYR706 4.2 47.0 1.0
CZ B:TYR706 4.4 42.9 1.0
CH2 B:TRP678 4.4 27.7 1.0
O1D B:HEM750 4.4 32.9 1.0
CD2 B:TYR706 4.6 37.8 1.0
C15 B:3XA800 4.6 59.3 1.0
F13 B:3XA800 4.7 63.6 1.0
O B:HOH1086 4.7 25.7 1.0
C14 B:3XA800 4.8 59.6 1.0
O1 B:3XA800 4.9 38.2 1.0
CZ3 B:TRP678 5.0 26.8 1.0

Fluorine binding site 5 out of 6 in 3nlv

Go back to Fluorine Binding Sites List in 3nlv
Fluorine binding site 5 out of 6 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-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-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-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:57.6
occ:1.00
 F8 B:3XA800 0.0 57.6 1.0
C6 B:3XA800 1.3 56.0 1.0
F7 B:3XA800 2.2 55.2 1.0
C5 B:3XA800 2.3 53.6 1.0
C11 B:3XA800 2.3 56.9 1.0
C16 B:3XA800 2.8 58.0 1.0
N4 B:3XA800 2.8 51.0 1.0
C3 B:3XA800 3.0 46.6 1.0
C12 B:3XA800 3.5 59.2 1.0
C2 B:3XA800 3.8 41.8 1.0
O B:HOH1197 4.0 42.9 1.0
C15 B:3XA800 4.2 59.3 1.0
O B:HOH1077 4.3 24.0 1.0
O B:HOH1086 4.4 25.7 1.0
O B:HOH1246 4.5 38.2 1.0
C13 B:3XA800 4.6 60.5 1.0
O2D B:HEM750 4.7 32.4 1.0
O B:HOH1236 4.8 32.6 1.0
C14 B:3XA800 4.9 59.6 1.0

Fluorine binding site 6 out of 6 in 3nlv

Go back to Fluorine Binding Sites List in 3nlv
Fluorine binding site 6 out of 6 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-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-(((3S,4S)-4-(2-(2,2-Difluoro-2-(3-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:63.6
occ:1.00
 F13 B:3XA800 0.0 63.6 1.0
C13 B:3XA800 1.3 60.5 1.0
C12 B:3XA800 2.3 59.2 1.0
C14 B:3XA800 2.4 59.6 1.0
CD2 B:LEU337 3.0 40.6 1.0
CZ B:TYR706 3.3 42.9 1.0
CE1 B:TYR706 3.5 43.5 1.0
CG B:LEU337 3.5 39.0 1.0
C11 B:3XA800 3.6 56.9 1.0
CE2 B:TYR706 3.6 40.4 1.0
C15 B:3XA800 3.6 59.3 1.0
O B:MET336 3.7 32.0 1.0
OH B:TYR706 3.7 47.0 1.0
CD1 B:TYR706 3.9 39.9 1.0
CD2 B:TYR706 4.0 37.8 1.0
C B:MET336 4.1 32.7 1.0
CG B:TYR706 4.1 35.2 1.0
C16 B:3XA800 4.1 58.0 1.0
CB B:MET336 4.1 32.6 1.0
NH1 B:ARG414 4.2 26.3 1.0
CD1 B:LEU337 4.5 43.1 1.0
CE B:MET336 4.5 38.0 1.0
N B:LEU337 4.6 35.2 1.0
CA B:MET336 4.6 31.8 1.0
CB B:LEU337 4.7 38.0 1.0
F7 B:3XA800 4.7 55.2 1.0
C6 B:3XA800 4.8 56.0 1.0
CA B:LEU337 4.9 37.8 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: Wed Jul 31 20:58:25 2024

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