Fluorine in PDB 8q11: Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(4-Fluorophenyl)-1, 2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2-Yn-1-Yl)Amino)Methyl) Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-126)

Enzymatic activity of Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(4-Fluorophenyl)-1, 2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2-Yn-1-Yl)Amino)Methyl) Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-126)

All present enzymatic activity of Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(4-Fluorophenyl)-1, 2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2-Yn-1-Yl)Amino)Methyl) Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-126):
3.4.23.22;

Protein crystallography data

The structure of Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(4-Fluorophenyl)-1, 2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2-Yn-1-Yl)Amino)Methyl) Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-126), PDB code: 8q11 was solved by J.M.Mueller, S.Eckelt, G.Klebe, S.Glinca, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.25 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.803, 72.529, 52.27, 90, 108.8, 90
R / Rfree (%) 15.4 / 17.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(4-Fluorophenyl)-1, 2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2-Yn-1-Yl)Amino)Methyl) Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-126) (pdb code 8q11). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(4-Fluorophenyl)-1, 2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2-Yn-1-Yl)Amino)Methyl) Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-126), PDB code: 8q11:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 8q11

Go back to Fluorine Binding Sites List in 8q11
Fluorine binding site 1 out of 2 in the Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(4-Fluorophenyl)-1, 2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2-Yn-1-Yl)Amino)Methyl) Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-126)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(4-Fluorophenyl)-1, 2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2-Yn-1-Yl)Amino)Methyl) Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-126) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:33.7
occ:1.00
 F22 A:IIZ401 0.0 33.7 1.0
C21 A:IIZ401 1.4 32.6 1.0
C20 A:IIZ401 2.4 31.3 1.0
C23 A:IIZ401 2.4 32.2 1.0
O A:HOH507 3.0 37.8 1.0
OXT A:ACT408 3.2 41.9 1.0
OD2 A:ASP119 3.2 28.9 1.0
CB A:SER115 3.6 22.6 1.0
CE1 A:PHE116 3.6 17.5 1.0
C19 A:IIZ401 3.7 30.2 1.0
CD1 A:PHE116 3.7 17.9 1.0
C24 A:IIZ401 3.7 30.9 1.0
O A:SER115 3.7 20.7 1.0
C A:SER115 3.8 20.2 1.0
C A:ACT408 3.9 42.0 1.0
N A:PHE116 4.1 17.8 1.0
C18 A:IIZ401 4.2 29.6 1.0
CZ A:PHE116 4.2 17.7 1.0
CG A:PHE116 4.3 16.7 1.0
CG A:ASP119 4.3 27.8 1.0
OG A:SER83 4.3 18.8 0.5
O A:ACT408 4.4 42.7 1.0
CA A:SER115 4.4 20.9 1.0
CA A:PHE116 4.4 17.5 1.0
OD2 A:ASP81 4.6 27.0 1.0
OG A:SER115 4.6 24.0 1.0
CE2 A:PHE116 4.7 17.7 1.0
CD2 A:PHE116 4.7 16.8 1.0
O A:HOH548 4.7 46.9 1.0
OG A:SER83 4.8 18.3 0.5
CB A:SER83 4.8 18.1 0.5
CH3 A:ACT408 4.8 41.7 1.0
CB A:SER83 4.8 17.8 0.5
CB A:PHE116 5.0 17.1 1.0

Fluorine binding site 2 out of 2 in 8q11

Go back to Fluorine Binding Sites List in 8q11
Fluorine binding site 2 out of 2 in the Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(4-Fluorophenyl)-1, 2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2-Yn-1-Yl)Amino)Methyl) Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-126)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(4-Fluorophenyl)-1, 2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2-Yn-1-Yl)Amino)Methyl) Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-126) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:45.8
occ:0.83
 F22 A:IIZ403 0.0 45.8 0.8
C21 A:IIZ403 1.4 45.6 0.8
C20 A:IIZ403 2.4 45.5 0.8
C23 A:IIZ403 2.4 45.5 0.8
N08 A:IIZ401 2.7 28.4 1.0
C07 A:IIZ401 2.9 30.2 1.0
CD1 A:ILE304 2.9 17.8 1.0
C06 A:IIZ401 3.1 33.7 1.0
C09 A:IIZ401 3.4 26.4 1.0
C24 A:IIZ403 3.7 45.8 0.8
C19 A:IIZ403 3.7 45.8 0.8
C27 A:IIZ401 3.8 25.1 1.0
CA A:GLY80 3.8 21.6 1.0
S29 A:IIZ401 3.9 28.0 1.0
C28 A:IIZ401 4.1 27.2 1.0
C18 A:IIZ403 4.1 46.5 0.8
OG1 A:THR222 4.2 14.1 1.0
C10 A:IIZ401 4.3 24.6 1.0
CG2 A:ILE300 4.3 32.3 1.0
CG1 A:ILE304 4.4 14.5 1.0
N A:GLY80 4.5 19.9 1.0
C A:GLY80 4.5 22.8 1.0
N04 A:IIZ401 4.6 37.0 1.0
C01 A:IIZ401 4.9 39.9 1.0
C02 A:IIZ401 4.9 40.0 1.0
CD1 A:ILE300 4.9 35.1 1.0
O A:GLY80 4.9 24.1 1.0
O11 A:IIZ401 4.9 24.4 1.0
OD2 A:ASP219 5.0 16.7 1.0

Reference:

J.M.Mueller, J.M.Mueller, S.Eckelt, G.Klebe, S.Glinca. N/A N/A.
Page generated: Sun Aug 11 11:20:10 2024

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