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Fluorine in PDB 4d2y: Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine

Enzymatic activity of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine

All present enzymatic activity of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine, PDB code: 4d2y was solved by H.Li, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.840 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.852, 110.465, 164.192, 90.00, 90.00, 90.00
R / Rfree (%) 17.05 / 20.83

Other elements in 4d2y:

The structure of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine 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 (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine (pdb code 4d2y). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine, PDB code: 4d2y:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4d2y

Go back to Fluorine Binding Sites List in 4d2y
Fluorine binding site 1 out of 2 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine


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 (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F800

b:74.1
occ:1.00
 F7' A:L5Z800 0.0 74.1 1.0
C3' A:L5Z800 1.3 74.0 1.0
C2' A:L5Z800 2.4 70.4 1.0
C4' A:L5Z800 2.4 70.8 1.0
CD2 A:LEU337 3.0 64.8 1.0
C1' A:L5Z800 3.6 63.6 1.0
C5' A:L5Z800 3.6 68.5 1.0
CB A:MET336 3.7 55.5 1.0
CG A:LEU337 3.7 67.3 1.0
CE A:MET336 3.9 57.2 1.0
CE2 A:TYR706 4.0 63.6 1.0
CZ A:TYR706 4.0 58.4 1.0
C6' A:L5Z800 4.1 67.9 1.0
OH A:TYR706 4.1 64.5 1.0
O A:MET336 4.3 42.2 1.0
C A:MET336 4.3 41.7 1.0
CD2 A:TYR706 4.5 65.3 1.0
SD A:MET336 4.5 84.5 1.0
CH2 B:TRP306 4.6 56.0 1.0
CE1 A:TYR706 4.6 47.1 1.0
CA A:MET336 4.6 40.4 1.0
CB A:LEU337 4.7 62.6 1.0
O A:HOH2076 4.7 63.1 1.0
N A:LEU337 4.7 45.8 1.0
CG A:MET336 4.7 68.4 1.0
CZ2 B:TRP306 4.8 44.4 1.0
CD1 A:LEU337 4.9 77.7 1.0
C24 A:L5Z800 4.9 57.6 1.0

Fluorine binding site 2 out of 2 in 4d2y

Go back to Fluorine Binding Sites List in 4d2y
Fluorine binding site 2 out of 2 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine


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 (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F800

b:84.0
occ:1.00
 F7' B:L5Z800 0.0 84.0 1.0
C3' B:L5Z800 1.3 76.1 1.0
C4' B:L5Z800 2.4 69.4 1.0
C2' B:L5Z800 2.4 69.1 1.0
CE2 B:TYR706 3.2 48.6 1.0
CD2 B:LEU337 3.2 59.9 1.0
CZ B:TYR706 3.3 45.4 1.0
OH B:TYR706 3.4 46.2 1.0
CG B:LEU337 3.6 56.4 1.0
O B:MET336 3.6 42.4 1.0
C5' B:L5Z800 3.6 69.4 1.0
C1' B:L5Z800 3.6 60.3 1.0
CB B:MET336 3.8 47.5 1.0
CD2 B:TYR706 3.9 46.9 1.0
C B:MET336 3.9 45.1 1.0
CE B:MET336 3.9 47.1 1.0
C6' B:L5Z800 4.1 63.2 1.0
CE1 B:TYR706 4.1 39.6 1.0
NH1 B:ARG414 4.2 36.5 1.0
CA B:MET336 4.4 42.8 1.0
CB B:LEU337 4.4 53.6 1.0
N B:LEU337 4.5 49.1 1.0
CG B:TYR706 4.6 35.6 1.0
CD1 B:TYR706 4.7 33.7 1.0
SD B:MET336 4.8 84.7 1.0
CD1 B:LEU337 4.8 60.2 1.0
CA B:LEU337 4.9 54.1 1.0
C24 B:L5Z800 4.9 52.9 1.0
CG B:MET336 4.9 52.5 1.0
CZ2 B:TRP678 4.9 40.9 1.0

Reference:

P.Mukherjee, H.Li, I.F.Sevrioukova, G.Chreifi, P.Martasek, L.J.Roman, T.L.Poulos, R.B.Silverman. Novel 2,4-Disubstituted Pyrimidines As Potent, Selective, and Cell-Permeable Inhibitors of Neuronal Nitric Oxide Synthase. J.Med.Chem. 2014.
ISSN: ESSN 1520-4804
PubMed: 25489882
DOI: 10.1021/JM501719E
Page generated: Mon Jul 14 21:02:39 2025

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