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Fluorine in PDB 4od0: Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Propanoylpiperidin-4-Yl)-3-[4-(Trifluoromethoxy)Phenyl]Urea

Enzymatic activity of Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Propanoylpiperidin-4-Yl)-3-[4-(Trifluoromethoxy)Phenyl]Urea

All present enzymatic activity of Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Propanoylpiperidin-4-Yl)-3-[4-(Trifluoromethoxy)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-Propanoylpiperidin-4-Yl)-3-[4-(Trifluoromethoxy)Phenyl]Urea, PDB code: 4od0 was solved by K.S.S.Lee, J.Liu, K.M.Wagner, S.Pakhomova, H.Dong, C.Morisseau, 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 / 2.92
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.136, 92.136, 243.354, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 25.2

Other elements in 4od0:

The structure of Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Propanoylpiperidin-4-Yl)-3-[4-(Trifluoromethoxy)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-Propanoylpiperidin-4-Yl)-3-[4-(Trifluoromethoxy)Phenyl]Urea (pdb code 4od0). 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-Propanoylpiperidin-4-Yl)-3-[4-(Trifluoromethoxy)Phenyl]Urea, PDB code: 4od0:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4od0

Go back to Fluorine Binding Sites List in 4od0
Fluorine binding site 1 out of 3 in the Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Propanoylpiperidin-4-Yl)-3-[4-(Trifluoromethoxy)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-Propanoylpiperidin-4-Yl)-3-[4-(Trifluoromethoxy)Phenyl]Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:36.4
occ:1.00
 F23 A:2RV603 0.0 36.4 1.0
C20 A:2RV603 1.3 34.5 1.0
F22 A:2RV603 2.1 33.4 1.0
F21 A:2RV603 2.1 32.8 1.0
O19 A:2RV603 2.2 35.4 1.0
C18 A:2RV603 2.8 39.1 1.0
C24 A:2RV603 3.4 38.5 1.0
CZ A:PHE387 3.5 38.8 1.0
CE1 A:PHE267 3.5 49.7 1.0
C17 A:2RV603 3.5 40.4 1.0
CD2 A:LEU428 3.6 53.8 1.0
CD2 A:LEU408 3.9 37.7 1.0
CE2 A:PHE387 4.1 38.4 1.0
CD1 A:PHE267 4.2 47.7 1.0
C25 A:2RV603 4.4 39.7 1.0
CG A:LEU428 4.5 56.6 1.0
CZ A:PHE267 4.6 49.9 1.0
CE1 A:PHE387 4.6 40.1 1.0
CD1 A:LEU428 4.6 57.4 1.0
C16 A:2RV603 4.6 39.6 1.0
C1 A:2RV603 5.0 39.7 1.0

Fluorine binding site 2 out of 3 in 4od0

Go back to Fluorine Binding Sites List in 4od0
Fluorine binding site 2 out of 3 in the Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Propanoylpiperidin-4-Yl)-3-[4-(Trifluoromethoxy)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-Propanoylpiperidin-4-Yl)-3-[4-(Trifluoromethoxy)Phenyl]Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:32.8
occ:1.00
 F21 A:2RV603 0.0 32.8 1.0
C20 A:2RV603 1.3 34.5 1.0
F23 A:2RV603 2.1 36.4 1.0
F22 A:2RV603 2.2 33.4 1.0
O19 A:2RV603 2.2 35.4 1.0
CD2 A:LEU428 3.0 53.8 1.0
CD1 A:LEU428 3.2 57.4 1.0
CG A:LEU428 3.2 56.6 1.0
CD2 A:LEU408 3.3 37.7 1.0
C18 A:2RV603 3.5 39.1 1.0
CD1 A:LEU417 3.8 63.4 1.0
SD A:MET419 3.9 67.3 1.0
C17 A:2RV603 4.2 40.4 1.0
C24 A:2RV603 4.4 38.5 1.0
CE A:MET419 4.6 65.4 1.0
CG A:LEU408 4.7 37.4 1.0
CB A:LEU428 4.7 56.5 1.0
CZ A:PHE387 4.8 38.8 1.0

Fluorine binding site 3 out of 3 in 4od0

Go back to Fluorine Binding Sites List in 4od0
Fluorine binding site 3 out of 3 in the Crystal Structure of Human Soluble Epoxide Hydrolase Complexed with 1- (1-Propanoylpiperidin-4-Yl)-3-[4-(Trifluoromethoxy)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-Propanoylpiperidin-4-Yl)-3-[4-(Trifluoromethoxy)Phenyl]Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:33.4
occ:1.00
 F22 A:2RV603 0.0 33.4 1.0
C20 A:2RV603 1.3 34.5 1.0
F23 A:2RV603 2.1 36.4 1.0
F21 A:2RV603 2.2 32.8 1.0
O19 A:2RV603 2.3 35.4 1.0
C17 A:2RV603 2.7 40.4 1.0
C18 A:2RV603 2.7 39.1 1.0
SD A:MET419 3.3 67.3 1.0
CD1 A:LEU428 3.7 57.4 1.0
CZ A:PHE387 3.7 38.8 1.0
CD1 A:TYR383 3.7 52.8 1.0
CG A:TYR383 3.9 52.6 1.0
CD2 A:LEU428 3.9 53.8 1.0
C24 A:2RV603 4.0 38.5 1.0
CB A:TYR383 4.0 52.9 1.0
C16 A:2RV603 4.0 39.6 1.0
CE A:MET419 4.3 65.4 1.0
CE2 A:PHE387 4.3 38.4 1.0
CG A:LEU428 4.3 56.6 1.0
CG A:MET419 4.3 67.0 1.0
CE1 A:TYR383 4.4 52.1 1.0
CE1 A:PHE387 4.7 40.1 1.0
CD2 A:TYR383 4.7 52.4 1.0
C25 A:2RV603 4.9 39.7 1.0
C1 A:2RV603 4.9 39.7 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: Sun Dec 13 12:09:32 2020

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