Fluorine in PDB 8q10: Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-(Hydroxymethyl) Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl) Pyrrolidin-3-Ol (Cbws-Se-125)

Enzymatic activity of Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-(Hydroxymethyl) Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl) Pyrrolidin-3-Ol (Cbws-Se-125)

All present enzymatic activity of Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-(Hydroxymethyl) Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl) Pyrrolidin-3-Ol (Cbws-Se-125):
3.4.23.22;

Protein crystallography data

The structure of Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-(Hydroxymethyl) Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl) Pyrrolidin-3-Ol (Cbws-Se-125), PDB code: 8q10 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) 27.97 / 1.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.857, 72.472, 52.427, 90, 109.17, 90
R / Rfree (%) 14.4 / 16.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-(Hydroxymethyl) Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl) Pyrrolidin-3-Ol (Cbws-Se-125) (pdb code 8q10). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-(Hydroxymethyl) Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl) Pyrrolidin-3-Ol (Cbws-Se-125), PDB code: 8q10:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8q10

Go back to Fluorine Binding Sites List in 8q10
Fluorine binding site 1 out of 3 in the Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-(Hydroxymethyl) Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl) Pyrrolidin-3-Ol (Cbws-Se-125)


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)-3-(2-(Hydroxymethyl) Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl) Pyrrolidin-3-Ol (Cbws-Se-125) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:34.2
occ:1.00
 F19 A:IJY401 0.0 34.2 1.0
C18 A:IJY401 1.3 32.9 1.0
F20 A:IJY401 2.2 34.1 1.0
F21 A:IJY401 2.2 32.1 1.0
C17 A:IJY401 2.3 32.0 1.0
C16 A:IJY401 2.7 31.0 1.0
CD1 A:PHE116 3.5 16.1 1.0
O A:SER115 3.5 18.9 1.0
C22 A:IJY401 3.6 32.2 1.0
CE1 A:PHE116 3.7 16.8 1.0
C A:SER115 3.9 18.0 1.0
CB A:ASP119 4.0 22.4 1.0
CA A:PHE116 4.0 15.9 1.0
C15 A:IJY401 4.1 29.9 1.0
OD2 A:ASP119 4.1 30.2 1.0
N A:PHE116 4.1 16.4 1.0
CG A:PHE116 4.2 16.0 1.0
O A:HOH570 4.3 34.9 1.0
CD1 A:ILE122 4.3 17.0 1.0
O A:HOH625 4.3 16.6 1.0
CG A:ASP119 4.5 27.3 1.0
CB A:SER115 4.6 20.5 1.0
CZ A:PHE116 4.6 17.9 1.0
CB A:PHE116 4.7 16.0 1.0
C23 A:IJY401 4.7 31.6 1.0
CA A:SER115 4.9 19.0 1.0
C14 A:IJY401 4.9 30.4 1.0

Fluorine binding site 2 out of 3 in 8q10

Go back to Fluorine Binding Sites List in 8q10
Fluorine binding site 2 out of 3 in the Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-(Hydroxymethyl) Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl) Pyrrolidin-3-Ol (Cbws-Se-125)


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)-3-(2-(Hydroxymethyl) Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl) Pyrrolidin-3-Ol (Cbws-Se-125) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:34.1
occ:1.00
 F20 A:IJY401 0.0 34.1 1.0
C18 A:IJY401 1.4 32.9 1.0
F19 A:IJY401 2.2 34.2 1.0
F21 A:IJY401 2.3 32.1 1.0
C17 A:IJY401 2.4 32.0 1.0
C22 A:IJY401 3.0 32.2 1.0
C16 A:IJY401 3.4 31.0 1.0
CB A:SER115 3.5 20.5 1.0
O A:HOH570 3.7 34.9 1.0
O A:SER115 3.9 18.9 1.0
O A:HOH612 3.9 41.3 1.0
OD2 A:ASP81 3.9 25.0 1.0
C A:SER115 4.1 18.0 1.0
C23 A:IJY401 4.3 31.6 1.0
OG A:SER115 4.3 22.6 1.0
OG A:SER83 4.3 18.6 0.5
CA A:SER115 4.4 19.0 1.0
C15 A:IJY401 4.5 29.9 1.0
N A:PHE116 4.7 16.4 1.0
C14 A:IJY401 4.9 30.4 1.0

Fluorine binding site 3 out of 3 in 8q10

Go back to Fluorine Binding Sites List in 8q10
Fluorine binding site 3 out of 3 in the Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-(Hydroxymethyl) Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl) Pyrrolidin-3-Ol (Cbws-Se-125)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-(Hydroxymethyl) Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl) Pyrrolidin-3-Ol (Cbws-Se-125) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:32.1
occ:1.00
 F21 A:IJY401 0.0 32.1 1.0
C18 A:IJY401 1.4 32.9 1.0
F19 A:IJY401 2.2 34.2 1.0
F20 A:IJY401 2.3 34.1 1.0
C17 A:IJY401 2.3 32.0 1.0
C22 A:IJY401 2.8 32.2 1.0
CB A:SER115 3.2 20.5 1.0
CD1 A:PHE116 3.2 16.1 1.0
N A:PHE116 3.3 16.4 1.0
C A:SER115 3.3 18.0 1.0
CE1 A:PHE116 3.4 16.8 1.0
OG A:SER83 3.4 18.6 0.5
CG A:PHE116 3.4 16.0 1.0
C16 A:IJY401 3.5 31.0 1.0
O A:SER115 3.6 18.9 1.0
CZ A:PHE116 3.6 17.9 1.0
CD2 A:PHE116 3.6 16.9 1.0
CE2 A:PHE116 3.7 17.7 1.0
CA A:PHE116 3.7 15.9 1.0
CB A:SER83 3.8 18.2 0.5
CB A:SER83 3.8 19.0 0.5
CA A:SER115 3.8 19.0 1.0
OG A:SER83 3.9 19.6 0.5
C23 A:IJY401 4.1 31.6 1.0
CB A:PHE116 4.2 16.0 1.0
OD2 A:ASP81 4.3 25.0 1.0
OG A:SER115 4.4 22.6 1.0
C15 A:IJY401 4.7 29.9 1.0
N A:SER115 4.8 18.8 1.0
O A:HOH570 4.8 34.9 1.0
C14 A:IJY401 4.9 30.4 1.0
O A:HOH612 4.9 41.3 1.0

Reference:

J.M.Mueller, J.M.Mueller, S.Eckelt, G.Klebe, S.Glinca. N/A N/A.
Page generated: Sun Aug 11 11:20:09 2024

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