Magnesium 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 / R_free (%)*	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:

Fluorine

(F)

3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total only one binding site of Magnesium was 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:

Magnesium binding site 1 out of 1 in 4od0

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Magnesium Binding Sites List in 4od0

Magnesium binding site 1 out of 1 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 Magnesium with other atoms in the Mg 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:Mg602 b:35.6 occ:1.00	O	A:HOH701	1.9	45.4	1.0
	OD2	A:ASP9	1.9	53.5	1.0
	O	A:HOH703	1.9	33.6	1.0
	OD1	A:ASP185	1.9	52.5	1.0
	O1	A:PO4601	2.0	36.5	1.0
	O	A:ASP11	2.2	55.0	1.0
	CG	A:ASP9	2.6	51.5	1.0
	OD1	A:ASP9	2.6	52.9	1.0
	CG	A:ASP185	3.0	50.9	1.0
	OD2	A:ASP185	3.3	52.9	1.0
	C	A:ASP11	3.3	52.8	1.0
	P	A:PO4601	3.4	38.9	1.0
	CB	A:ASP11	3.9	55.6	1.0
	CA	A:ASP11	3.9	52.6	1.0
	N	A:ASP11	4.0	51.6	1.0
	O4	A:PO4601	4.0	36.0	1.0
	CB	A:ASP9	4.0	50.1	1.0
	OD1	A:ASP184	4.1	47.6	1.0
	O3	A:PO4601	4.1	36.4	1.0
	CB	A:ASP185	4.3	49.3	1.0
	N	A:ASP185	4.4	50.1	1.0
	N	A:GLY12	4.4	51.8	1.0
	O2	A:PO4601	4.4	37.2	1.0
	NZ	A:LYS160	4.5	45.9	1.0
	CG	A:ASP184	4.6	48.9	1.0
	OD1	A:ASP11	4.7	59.7	1.0
	C	A:LEU10	4.7	49.9	1.0
	CA	A:GLY12	4.8	53.3	1.0
	CG	A:ASP11	4.8	56.2	1.0
	N	A:LEU10	4.8	51.2	1.0
	OD2	A:ASP184	4.9	47.2	1.0
	CA	A:ASP185	4.9	50.3	1.0
	CD1	A:ILE186	4.9	54.3	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: Tue Aug 20 00:47:11 2024

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