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Fluorine in PDB 4y2s: Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Phenyl]-1H-Pyrazol-4-Ol

Enzymatic activity of Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Phenyl]-1H-Pyrazol-4-Ol

All present enzymatic activity of Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Phenyl]-1H-Pyrazol-4-Ol:
3.3.2.10;

Protein crystallography data

The structure of Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Phenyl]-1H-Pyrazol-4-Ol, PDB code: 4y2s 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) 76.29 / 2.30
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.739, 92.739, 244.196, 90.00, 90.00, 120.00
R / Rfree (%) 19.5 / 23.3

Other elements in 4y2s:

The structure of Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Phenyl]-1H-Pyrazol-4-Ol 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)Phenyl]-1H-Pyrazol-4-Ol (pdb code 4y2s). 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)Phenyl]-1H-Pyrazol-4-Ol, PDB code: 4y2s:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4y2s

Go back to Fluorine Binding Sites List in 4y2s
Fluorine binding site 1 out of 3 in the Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Phenyl]-1H-Pyrazol-4-Ol


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)Phenyl]-1H-Pyrazol-4-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:43.6
occ:1.00
 F10 A:49P602 0.0 43.6 1.0
C4 A:49P602 1.3 41.0 1.0
F12 A:49P602 2.1 40.4 1.0
F11 A:49P602 2.2 42.2 1.0
C8 A:49P602 2.4 42.0 1.0
C15 A:49P602 2.7 39.5 1.0
CE2 A:TYR383 3.5 26.3 1.0
CD1 A:PHE267 3.5 14.3 1.0
CE1 A:PHE267 3.5 14.7 1.0
C9 A:49P602 3.6 43.8 1.0
CD2 A:TYR383 3.7 25.9 1.0
CE2 A:PHE387 3.7 21.2 1.0
CZ A:PHE387 3.8 20.1 1.0
OH A:TYR466 3.9 18.9 1.0
C16 A:49P602 4.1 43.1 1.0
CZ A:TYR383 4.5 29.6 1.0
O A:PHE267 4.7 15.4 1.0
C7 A:49P602 4.7 47.0 1.0
CG A:TYR383 4.8 26.0 1.0
CZ A:TYR466 4.8 18.4 1.0
CG A:PHE267 4.8 13.7 1.0
CZ A:PHE267 4.8 13.9 1.0
O A:HOH715 4.9 23.8 1.0
OH A:TYR383 4.9 29.7 1.0
C14 A:49P602 4.9 43.5 1.0

Fluorine binding site 2 out of 3 in 4y2s

Go back to Fluorine Binding Sites List in 4y2s
Fluorine binding site 2 out of 3 in the Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Phenyl]-1H-Pyrazol-4-Ol


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)Phenyl]-1H-Pyrazol-4-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:42.2
occ:1.00
 F11 A:49P602 0.0 42.2 1.0
C4 A:49P602 1.4 41.0 1.0
F10 A:49P602 2.2 43.6 1.0
F12 A:49P602 2.2 40.4 1.0
C8 A:49P602 2.4 42.0 1.0
C9 A:49P602 2.8 43.8 1.0
CD2 A:LEU408 3.4 19.1 1.0
C15 A:49P602 3.6 39.5 1.0
SD A:MET419 3.9 51.4 1.0
C7 A:49P602 4.2 47.0 1.0
CD2 A:LEU428 4.3 34.3 1.0
CD2 A:TYR383 4.5 25.9 1.0
CE A:MET419 4.6 53.7 1.0
CG A:LEU428 4.7 34.9 1.0
CD1 A:LEU428 4.7 32.9 1.0
C16 A:49P602 4.7 43.1 1.0
CZ A:PHE387 4.8 20.1 1.0
CE2 A:TYR383 4.8 26.3 1.0
CG A:LEU408 4.8 19.6 1.0
C14 A:49P602 4.9 43.5 1.0
CE1 A:PHE267 4.9 14.7 1.0

Fluorine binding site 3 out of 3 in 4y2s

Go back to Fluorine Binding Sites List in 4y2s
Fluorine binding site 3 out of 3 in the Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Phenyl]-1H-Pyrazol-4-Ol


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)Phenyl]-1H-Pyrazol-4-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:40.4
occ:1.00
 F12 A:49P602 0.0 40.4 1.0
C4 A:49P602 1.3 41.0 1.0
F10 A:49P602 2.1 43.6 1.0
F11 A:49P602 2.2 42.2 1.0
C8 A:49P602 2.3 42.0 1.0
C15 A:49P602 3.1 39.5 1.0
C9 A:49P602 3.2 43.8 1.0
CH2 A:TRP525 3.6 17.7 1.0
CD1 A:PHE267 3.7 14.3 1.0
CD2 A:LEU408 3.7 19.1 1.0
O A:PHE267 3.8 15.4 1.0
CE1 A:PHE267 3.8 14.7 1.0
CD A:PRO268 3.8 16.3 1.0
CZ2 A:TRP525 4.1 17.2 1.0
CD1 A:LEU408 4.4 18.4 1.0
C16 A:49P602 4.4 43.1 1.0
C7 A:49P602 4.4 47.0 1.0
C A:PHE267 4.5 15.3 1.0
CG A:LEU408 4.6 19.6 1.0
CG A:PRO268 4.6 17.4 1.0
N A:PRO268 4.7 15.8 1.0
CZ3 A:TRP525 4.8 17.0 1.0
C14 A:49P602 4.9 43.5 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 01:37:18 2025

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