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Fluorine in PDB 4y2q: Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine

Enzymatic activity of Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine

All present enzymatic activity of Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine:
3.3.2.10;

Protein crystallography data

The structure of Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine, PDB code: 4y2q was solved by Y.Amano, T.Yamaguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.13 / 2.40
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.544, 92.544, 243.634, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 25.7

Other elements in 4y2q:

The structure of Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine (pdb code 4y2q). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine, PDB code: 4y2q:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4y2q

Go back to Fluorine Binding Sites List in 4y2q
Fluorine binding site 1 out of 3 in the Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:34.7
occ:1.00
 F11 A:49N602 0.0 34.7 1.0
C6 A:49N602 1.3 32.5 1.0
F12 A:49N602 2.1 32.8 1.0
F13 A:49N602 2.2 36.8 1.0
C2 A:49N602 2.3 34.3 1.0
C5 A:49N602 2.6 35.1 1.0
CD2 A:LEU408 3.1 22.6 1.0
C1 A:49N602 3.6 34.6 1.0
CD2 A:LEU428 3.8 37.8 1.0
SD A:MET419 3.8 45.2 1.0
C10 A:49N602 4.0 37.6 1.0
CD1 A:LEU428 4.0 34.6 1.0
CG A:LEU428 4.1 37.1 1.0
N3 A:49N602 4.2 32.6 1.0
CE A:MET419 4.2 46.8 1.0
CD2 A:LEU417 4.5 61.8 1.0
CG A:LEU408 4.6 23.1 1.0
C7 A:49N602 4.6 32.0 1.0
CZ A:PHE387 4.6 25.1 1.0
N4 A:49N602 4.7 33.1 1.0
C9 A:49N602 4.8 34.9 1.0
CE1 A:PHE267 4.8 21.3 1.0
CD1 A:LEU408 4.9 23.2 1.0

Fluorine binding site 2 out of 3 in 4y2q

Go back to Fluorine Binding Sites List in 4y2q
Fluorine binding site 2 out of 3 in the Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:32.8
occ:1.00
 F12 A:49N602 0.0 32.8 1.0
C6 A:49N602 1.3 32.5 1.0
F13 A:49N602 2.1 36.8 1.0
F11 A:49N602 2.1 34.7 1.0
C2 A:49N602 2.4 34.3 1.0
C7 A:49N602 3.1 32.0 1.0
C5 A:49N602 3.2 35.1 1.0
C1 A:49N602 3.2 34.6 1.0
N3 A:49N602 3.4 32.6 1.0
CD2 A:LEU408 3.5 22.6 1.0
CE1 A:PHE267 3.7 21.3 1.0
CD1 A:PHE267 3.8 22.2 1.0
C14 A:49N602 3.8 33.5 1.0
CD A:PRO268 3.9 21.9 1.0
CH2 A:TRP525 4.0 20.0 1.0
O A:PHE267 4.2 20.8 1.0
CD1 A:LEU408 4.3 23.2 1.0
CZ2 A:TRP525 4.4 19.6 1.0
N4 A:49N602 4.4 33.1 1.0
C10 A:49N602 4.5 37.6 1.0
CG A:LEU408 4.5 23.1 1.0
CG A:PRO268 4.5 21.7 1.0
C A:PHE267 4.8 21.5 1.0
N A:PRO268 4.8 20.1 1.0
C8 A:49N602 4.8 32.0 1.0
C9 A:49N602 4.9 34.9 1.0
CZ A:PHE267 5.0 21.5 1.0

Fluorine binding site 3 out of 3 in 4y2q

Go back to Fluorine Binding Sites List in 4y2q
Fluorine binding site 3 out of 3 in the Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:36.8
occ:1.00
 F13 A:49N602 0.0 36.8 1.0
C6 A:49N602 1.4 32.5 1.0
F12 A:49N602 2.1 32.8 1.0
F11 A:49N602 2.2 34.7 1.0
C2 A:49N602 2.4 34.3 1.0
N3 A:49N602 2.7 32.6 1.0
C1 A:49N602 2.9 34.6 1.0
C7 A:49N602 3.1 32.0 1.0
C14 A:49N602 3.3 33.5 1.0
C5 A:49N602 3.6 35.1 1.0
C8 A:49N602 3.9 32.0 1.0
CD2 A:TYR383 4.0 35.8 1.0
CE2 A:TYR383 4.0 36.6 1.0
CE1 A:PHE267 4.0 21.3 1.0
CZ A:PHE387 4.1 25.1 1.0
SD A:MET419 4.2 45.2 1.0
CD1 A:PHE267 4.2 22.2 1.0
C15 A:49N602 4.2 30.4 1.0
CE2 A:PHE387 4.2 23.6 1.0
N4 A:49N602 4.2 33.1 1.0
N16 A:49N602 4.3 32.3 1.0
C10 A:49N602 4.7 37.6 1.0
CG A:TYR383 4.8 37.2 1.0
CZ A:TYR383 4.8 39.6 1.0
C9 A:49N602 4.9 34.9 1.0
CD2 A:LEU408 5.0 22.6 1.0
OH A:TYR466 5.0 39.0 1.0

Reference:

Y.Amano, E.Tanabe, T.Yamaguchi. Identification of N-Ethylmethylamine As A Novel Scaffold For Inhibitors of Soluble Epoxide Hydrolase By Crystallographic Fragment Screening Bioorg.Med.Chem. V. 23 2310 2015.
ISSN: ESSN 1464-3391
PubMed: 25862210
DOI: 10.1016/J.BMC.2015.03.083
Page generated: Tue Jul 15 01:37:15 2025

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