Atomistry » Fluorine » PDB 6yhc-6z4b » 6yl4
Atomistry »
  Fluorine »
    PDB 6yhc-6z4b »
      6yl4 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy