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Fluorine in PDB 4ocz: Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Isobutyrylpiperidin-4-Yl)-3-(4-(Trifluoromethyl)Phenyl)Urea

Enzymatic activity of Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Isobutyrylpiperidin-4-Yl)-3-(4-(Trifluoromethyl)Phenyl)Urea

All present enzymatic activity of Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Isobutyrylpiperidin-4-Yl)-3-(4-(Trifluoromethyl)Phenyl)Urea:
3.1.3.76; 3.3.2.10;

Protein crystallography data

The structure of Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Isobutyrylpiperidin-4-Yl)-3-(4-(Trifluoromethyl)Phenyl)Urea, PDB code: 4ocz was solved by K.S.S.Lee, J.Liu, K.M.Wagner, S.Pakhomova, H.Dong, C.Morriseau, S.H.Fu, J.Yang, P.Wang, A.Ulu, C.Mate, L.Nguyen, H.Wullf, M.L.Eldin, A.A.Mara, M.E.Newcomer, D.C.Zeldin, B.D.Hammock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.94
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.229, 92.229, 243.373, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 26.9

Other elements in 4ocz:

The structure of Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Isobutyrylpiperidin-4-Yl)-3-(4-(Trifluoromethyl)Phenyl)Urea also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Isobutyrylpiperidin-4-Yl)-3-(4-(Trifluoromethyl)Phenyl)Urea (pdb code 4ocz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Isobutyrylpiperidin-4-Yl)-3-(4-(Trifluoromethyl)Phenyl)Urea, PDB code: 4ocz:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4ocz

Go back to Fluorine Binding Sites List in 4ocz
Fluorine binding site 1 out of 3 in the Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Isobutyrylpiperidin-4-Yl)-3-(4-(Trifluoromethyl)Phenyl)Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Isobutyrylpiperidin-4-Yl)-3-(4-(Trifluoromethyl)Phenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:67.9
occ:1.00
 F23 A:2RU603 0.0 67.9 1.0
C20 A:2RU603 1.3 68.7 1.0
F22 A:2RU603 2.0 77.3 1.0
F21 A:2RU603 2.2 67.3 1.0
C19 A:2RU603 2.3 65.9 1.0
C24 A:2RU603 3.1 66.7 1.0
C18 A:2RU603 3.3 63.0 1.0
CZ A:PHE387 3.6 63.0 1.0
CD2 A:LEU428 3.7 71.1 1.0
CE1 A:PHE267 3.9 77.7 1.0
CD1 A:PHE267 4.1 74.3 1.0
CE2 A:PHE387 4.1 63.6 1.0
CD1 A:LEU428 4.3 70.5 1.0
C25 A:2RU603 4.3 70.7 1.0
CD2 A:LEU408 4.3 65.2 1.0
C17 A:2RU603 4.5 67.5 1.0
CG A:LEU428 4.6 70.5 1.0
CE1 A:PHE387 4.6 63.4 1.0
CD1 A:LEU408 4.7 61.5 1.0
C1 A:2RU603 5.0 68.5 1.0

Fluorine binding site 2 out of 3 in 4ocz

Go back to Fluorine Binding Sites List in 4ocz
Fluorine binding site 2 out of 3 in the Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Isobutyrylpiperidin-4-Yl)-3-(4-(Trifluoromethyl)Phenyl)Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Isobutyrylpiperidin-4-Yl)-3-(4-(Trifluoromethyl)Phenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:67.3
occ:1.00
 F21 A:2RU603 0.0 67.3 1.0
C20 A:2RU603 1.3 68.7 1.0
F23 A:2RU603 2.2 67.9 1.0
F22 A:2RU603 2.2 77.3 1.0
C19 A:2RU603 2.3 65.9 1.0
C18 A:2RU603 2.7 63.0 1.0
CD2 A:LEU408 3.0 65.2 1.0
C24 A:2RU603 3.5 66.7 1.0
CD1 A:LEU408 3.7 61.5 1.0
CG A:LEU408 3.9 64.4 1.0
C17 A:2RU603 4.1 67.5 1.0
CZ2 A:TRP525 4.2 57.4 1.0
CD2 A:LEU417 4.4 90.7 1.0
CH2 A:TRP525 4.5 58.7 1.0
CB A:LEU408 4.6 64.3 1.0
C25 A:2RU603 4.6 70.7 1.0
CD1 A:PHE267 4.9 74.3 1.0
C1 A:2RU603 4.9 68.5 1.0
CD2 A:LEU428 4.9 71.1 1.0
CD A:PRO268 4.9 53.2 1.0

Fluorine binding site 3 out of 3 in 4ocz

Go back to Fluorine Binding Sites List in 4ocz
Fluorine binding site 3 out of 3 in the Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Isobutyrylpiperidin-4-Yl)-3-(4-(Trifluoromethyl)Phenyl)Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Isobutyrylpiperidin-4-Yl)-3-(4-(Trifluoromethyl)Phenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:77.3
occ:1.00
 F22 A:2RU603 0.0 77.3 1.0
C20 A:2RU603 1.3 68.7 1.0
F23 A:2RU603 2.0 67.9 1.0
F21 A:2RU603 2.2 67.3 1.0
C19 A:2RU603 2.2 65.9 1.0
C24 A:2RU603 2.6 66.7 1.0
C18 A:2RU603 3.5 63.0 1.0
C25 A:2RU603 3.9 70.7 1.0
CD1 A:LEU428 4.0 70.5 1.0
CD2 A:LEU417 4.4 90.7 1.0
CD2 A:LEU408 4.5 65.2 1.0
CD2 A:LEU428 4.6 71.1 1.0
C17 A:2RU603 4.6 67.5 1.0
CZ A:PHE387 4.8 63.0 1.0
C1 A:2RU603 4.8 68.5 1.0
CG A:LEU428 4.8 70.5 1.0

Reference:

K.S.Lee, J.Y.Liu, K.M.Wagner, S.Pakhomova, H.Dong, C.Morisseau, S.H.Fu, J.Yang, P.Wang, A.Ulu, C.A.Mate, L.V.Nguyen, S.H.Hwang, M.L.Edin, A.A.Mara, H.Wulff, M.E.Newcomer, D.C.Zeldin, B.D.Hammock. Optimized Inhibitors of Soluble Epoxide Hydrolase Improve in Vitro Target Residence Time and in Vivo Efficacy. J.Med.Chem. V. 57 7016 2014.
ISSN: ISSN 0022-2623
PubMed: 25079952
DOI: 10.1021/JM500694P
Page generated: Thu Aug 1 04:30:25 2024

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