Atomistry » Fluorine » PDB 6yhd-6z4d » 6yl4
Atomistry »
  Fluorine »
    PDB 6yhd-6z4d »
      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: Tue Jul 15 17:52:20 2025

Last articles

Mg in 6KD7
Mg in 6KCM
Mg in 6KCK
Mg in 6KCL
Mg in 6KCC
Mg in 6KCA
Mg in 6KC0
Mg in 6KBZ
Mg in 6KAL
Mg in 6KAK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy