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Fluorine in PDB 6yl4: Soluble Epoxide Hydrolase in Complex with 3-((R)-3-(1-Hydroxyureido) But-1-Yn-1-Yl)-N-((S)-3-Phenyl-3-(4-Trifluoromethoxy)Phenyl)Propyl) Benzamide

Enzymatic activity of Soluble Epoxide Hydrolase in Complex with 3-((R)-3-(1-Hydroxyureido) But-1-Yn-1-Yl)-N-((S)-3-Phenyl-3-(4-Trifluoromethoxy)Phenyl)Propyl) Benzamide

All present enzymatic activity of Soluble Epoxide Hydrolase in Complex with 3-((R)-3-(1-Hydroxyureido) But-1-Yn-1-Yl)-N-((S)-3-Phenyl-3-(4-Trifluoromethoxy)Phenyl)Propyl) Benzamide:
3.1.3.76; 3.3.2.10;

Protein crystallography data

The structure of Soluble Epoxide Hydrolase in Complex with 3-((R)-3-(1-Hydroxyureido) But-1-Yn-1-Yl)-N-((S)-3-Phenyl-3-(4-Trifluoromethoxy)Phenyl)Propyl) Benzamide, PDB code: 6yl4 was solved by J.S.Kramer, D.Pogoryelov, K.Hiesinger, E.Proschak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.12 / 2.00
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 79.934, 92.238, 106.646, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 20.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Soluble Epoxide Hydrolase in Complex with 3-((R)-3-(1-Hydroxyureido) But-1-Yn-1-Yl)-N-((S)-3-Phenyl-3-(4-Trifluoromethoxy)Phenyl)Propyl) Benzamide (pdb code 6yl4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Soluble Epoxide Hydrolase in Complex with 3-((R)-3-(1-Hydroxyureido) But-1-Yn-1-Yl)-N-((S)-3-Phenyl-3-(4-Trifluoromethoxy)Phenyl)Propyl) Benzamide, PDB code: 6yl4:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6yl4

Go back to Fluorine Binding Sites List in 6yl4
Fluorine binding site 1 out of 3 in the Soluble Epoxide Hydrolase in Complex with 3-((R)-3-(1-Hydroxyureido) But-1-Yn-1-Yl)-N-((S)-3-Phenyl-3-(4-Trifluoromethoxy)Phenyl)Propyl) Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Soluble Epoxide Hydrolase in Complex with 3-((R)-3-(1-Hydroxyureido) But-1-Yn-1-Yl)-N-((S)-3-Phenyl-3-(4-Trifluoromethoxy)Phenyl)Propyl) Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:0.1
occ:1.00
 F01 A:OWW601 0.0 0.1 1.0
C02 A:OWW601 1.4 0.6 1.0
F04 A:OWW601 2.2 0.4 1.0
F03 A:OWW601 2.2 0.1 1.0
O05 A:OWW601 2.3 0.6 1.0
CD1 A:PHE497 3.3 59.9 1.0
C06 A:OWW601 3.6 89.0 1.0
CB A:PHE497 3.8 54.7 1.0
CG A:PHE497 3.9 59.5 1.0
O A:HOH756 4.1 46.7 1.0
C07 A:OWW601 4.2 77.4 1.0
OG A:SER412 4.2 62.9 1.0
OG A:SER415 4.2 79.5 1.0
N A:PHE497 4.2 43.2 1.0
CE1 A:PHE497 4.3 68.5 1.0
O A:HOH762 4.4 57.4 1.0
O A:LYS495 4.4 42.2 1.0
CA A:PHE497 4.6 49.1 1.0
C38 A:OWW601 4.6 79.7 1.0
CB A:SER415 4.7 76.4 1.0
CB A:SER412 4.9 64.4 1.0
CA A:SER412 5.0 56.6 1.0

Fluorine binding site 2 out of 3 in 6yl4

Go back to Fluorine Binding Sites List in 6yl4
Fluorine binding site 2 out of 3 in the Soluble Epoxide Hydrolase in Complex with 3-((R)-3-(1-Hydroxyureido) But-1-Yn-1-Yl)-N-((S)-3-Phenyl-3-(4-Trifluoromethoxy)Phenyl)Propyl) Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Soluble Epoxide Hydrolase in Complex with 3-((R)-3-(1-Hydroxyureido) But-1-Yn-1-Yl)-N-((S)-3-Phenyl-3-(4-Trifluoromethoxy)Phenyl)Propyl) Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:0.1
occ:1.00
 F03 A:OWW601 0.0 0.1 1.0
C02 A:OWW601 1.4 0.6 1.0
F04 A:OWW601 2.2 0.4 1.0
F01 A:OWW601 2.2 0.1 1.0
O05 A:OWW601 2.3 0.6 1.0
C07 A:OWW601 2.7 77.4 1.0
N A:PHE497 2.9 43.2 1.0
C06 A:OWW601 2.9 89.0 1.0
OD2 A:ASP496 3.4 41.2 1.0
CB A:PHE497 3.6 54.7 1.0
CA A:PHE497 3.6 49.1 1.0
N A:VAL498 3.6 46.3 1.0
C A:ASP496 3.8 43.4 1.0
C A:PHE497 3.9 47.8 1.0
CA A:ASP496 3.9 38.3 1.0
CG2 A:VAL498 4.1 52.0 1.0
C08 A:OWW601 4.1 71.4 1.0
O A:LYS495 4.1 42.2 1.0
O A:HOH756 4.2 46.7 1.0
CG A:PHE497 4.2 59.5 1.0
C38 A:OWW601 4.3 79.7 1.0
CD1 A:PHE497 4.3 59.9 1.0
CG A:ASP496 4.3 44.2 1.0
CB A:HIS524 4.3 39.7 1.0
CB A:VAL498 4.5 55.1 1.0
CA A:VAL498 4.7 52.3 1.0
CB A:ASP496 4.8 44.4 1.0
O A:ASP496 4.9 45.2 1.0
OG A:SER412 4.9 62.9 1.0
N A:HIS524 4.9 38.1 1.0
O A:PHE497 5.0 53.0 1.0
N A:ASP496 5.0 38.8 1.0
C A:LYS495 5.0 50.4 1.0

Fluorine binding site 3 out of 3 in 6yl4

Go back to Fluorine Binding Sites List in 6yl4
Fluorine binding site 3 out of 3 in the Soluble Epoxide Hydrolase in Complex with 3-((R)-3-(1-Hydroxyureido) But-1-Yn-1-Yl)-N-((S)-3-Phenyl-3-(4-Trifluoromethoxy)Phenyl)Propyl) Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Soluble Epoxide Hydrolase in Complex with 3-((R)-3-(1-Hydroxyureido) But-1-Yn-1-Yl)-N-((S)-3-Phenyl-3-(4-Trifluoromethoxy)Phenyl)Propyl) Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:0.4
occ:1.00
 F04 A:OWW601 0.0 0.4 1.0
C02 A:OWW601 1.4 0.6 1.0
F01 A:OWW601 2.2 0.1 1.0
F03 A:OWW601 2.2 0.1 1.0
O05 A:OWW601 2.3 0.6 1.0
C06 A:OWW601 2.7 89.0 1.0
C07 A:OWW601 2.9 77.4 1.0
CE A:MET419 3.5 86.7 1.0
CG2 A:VAL498 3.7 52.0 1.0
C38 A:OWW601 3.7 79.7 1.0
CG A:MET419 4.0 82.0 1.0
C08 A:OWW601 4.0 71.4 1.0
CB A:PHE497 4.3 54.7 1.0
SD A:MET419 4.5 95.9 1.0
N A:VAL498 4.6 46.3 1.0
C37 A:OWW601 4.7 70.5 1.0
N A:PHE497 4.7 43.2 1.0
CB A:VAL498 4.8 55.1 1.0
C A:PHE497 4.8 47.8 1.0
C09 A:OWW601 4.8 69.2 1.0
CA A:PHE497 4.8 49.1 1.0
CD1 A:PHE497 4.9 59.9 1.0
OG A:SER415 5.0 79.5 1.0

Reference:

K.Hiesinger, J.S.Kramer, S.Beyer, T.Eckes, S.Brunst, C.Flauaus, S.K.Wittmann, L.Weizel, A.Kaiser, S.B.M.Kretschmer, S.George, C.Angioni, J.Heering, G.Geisslinger, M.Schubert-Zsilavecz, A.Schmidtko, D.Pogoryelov, J.Pfeilschifter, B.Hofmann, D.Steinhilber, S.Schwalm, E.Proschak. Design, Synthesis, and Structure-Activity Relationship Studies of Dual Inhibitors of Soluble Epoxide Hydrolase and 5-Lipoxygenase. J.Med.Chem. V. 63 11498 2020.
ISSN: ISSN 0022-2623
PubMed: 33044073
DOI: 10.1021/ACS.JMEDCHEM.0C00561
Page generated: Fri Aug 2 04:42:19 2024

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