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Fluorine in PDB 8q0x: Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-((Methyl(Propyl) Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4- Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-087)

Enzymatic activity of Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-((Methyl(Propyl) Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4- Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-087)

All present enzymatic activity of Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-((Methyl(Propyl) Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4- Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-087):
3.4.23.22;

Protein crystallography data

The structure of Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-((Methyl(Propyl) Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4- Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-087), PDB code: 8q0x 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) 34.51 / 1.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.923, 72.561, 52.503, 90, 109.19, 90
R / Rfree (%) 14.3 / 16.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-((Methyl(Propyl) Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4- Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-087) (pdb code 8q0x). 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-((Methyl(Propyl) Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4- Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-087), PDB code: 8q0x:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8q0x

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Fluorine binding site 1 out of 3 in the Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-((Methyl(Propyl) Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4- Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-087)


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-((Methyl(Propyl) Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4- Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-087) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:30.1
occ:1.00
 F23 A:IL4402 0.0 30.1 1.0
C22 A:IL4402 1.4 28.7 1.0
F24 A:IL4402 2.2 27.8 1.0
F25 A:IL4402 2.2 30.1 1.0
C21 A:IL4402 2.4 26.8 1.0
C20 A:IL4402 3.0 26.4 1.0
C26 A:IL4402 3.4 25.7 1.0
CB A:SER115 3.6 20.9 1.0
O A:HOH585 3.7 38.1 1.0
O A:SER115 3.8 17.9 1.0
OD2 A:ASP81 4.0 26.2 1.0
O A:HOH542 4.1 36.8 1.0
C A:SER115 4.1 17.2 1.0
C19 A:IL4402 4.3 25.8 1.0
CA A:SER115 4.4 18.6 1.0
OG A:SER115 4.5 23.3 1.0
OG A:SER83 4.5 19.1 0.5
C27 A:IL4402 4.6 26.1 1.0
N A:PHE116 4.7 15.9 1.0
C18 A:IL4402 4.9 26.3 1.0

Fluorine binding site 2 out of 3 in 8q0x

Go back to Fluorine Binding Sites List in 8q0x
Fluorine binding site 2 out of 3 in the Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-((Methyl(Propyl) Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4- Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-087)


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-((Methyl(Propyl) Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4- Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-087) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:27.8
occ:1.00
 F24 A:IL4402 0.0 27.8 1.0
C22 A:IL4402 1.3 28.7 1.0
F23 A:IL4402 2.2 30.1 1.0
F25 A:IL4402 2.2 30.1 1.0
C21 A:IL4402 2.3 26.8 1.0
C20 A:IL4402 2.8 26.4 1.0
CB A:SER115 3.2 20.9 1.0
CD1 A:PHE116 3.3 15.9 1.0
C A:SER115 3.3 17.2 1.0
N A:PHE116 3.4 15.9 1.0
CE1 A:PHE116 3.4 16.5 1.0
CG A:PHE116 3.5 15.6 1.0
OG A:SER83 3.5 19.1 0.5
C26 A:IL4402 3.5 25.7 1.0
O A:SER115 3.6 17.9 1.0
CZ A:PHE116 3.6 17.3 1.0
CD2 A:PHE116 3.8 16.8 1.0
CA A:PHE116 3.8 15.3 1.0
CE2 A:PHE116 3.9 17.4 1.0
CB A:SER83 3.9 19.1 0.5
CB A:SER83 3.9 20.7 0.5
CA A:SER115 3.9 18.6 1.0
OG A:SER83 4.0 21.4 0.5
C19 A:IL4402 4.1 25.8 1.0
OD2 A:ASP81 4.2 26.2 1.0
CB A:PHE116 4.2 15.2 1.0
OG A:SER115 4.5 23.3 1.0
C27 A:IL4402 4.6 26.1 1.0
O A:HOH585 4.8 38.1 1.0
C18 A:IL4402 4.8 26.3 1.0
N A:SER115 4.9 18.8 1.0
O A:HOH542 4.9 36.8 1.0

Fluorine binding site 3 out of 3 in 8q0x

Go back to Fluorine Binding Sites List in 8q0x
Fluorine binding site 3 out of 3 in the Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-((Methyl(Propyl) Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4- Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-087)


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-((Methyl(Propyl) Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2,4- Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-087) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:30.1
occ:1.00
 F25 A:IL4402 0.0 30.1 1.0
C22 A:IL4402 1.4 28.7 1.0
F24 A:IL4402 2.2 27.8 1.0
F23 A:IL4402 2.2 30.1 1.0
C21 A:IL4402 2.4 26.8 1.0
C26 A:IL4402 2.8 25.7 1.0
CD1 A:PHE116 3.4 15.9 1.0
O A:SER115 3.5 17.9 1.0
C20 A:IL4402 3.6 26.4 1.0
CE1 A:PHE116 3.7 16.5 1.0
CB A:ASP119 3.9 21.4 1.0
C A:SER115 4.0 17.2 1.0
CA A:PHE116 4.0 15.3 1.0
O A:HOH654 4.2 16.2 1.0
N A:PHE116 4.2 15.9 1.0
C27 A:IL4402 4.2 26.1 1.0
OD2 A:ASP119 4.2 29.6 1.0
CD1 A:ILE122 4.2 17.2 1.0
CG A:PHE116 4.2 15.6 1.0
O A:HOH585 4.3 38.1 1.0
CG A:ASP119 4.5 26.3 1.0
CZ A:PHE116 4.6 17.3 1.0
CB A:SER115 4.7 20.9 1.0
CB A:PHE116 4.7 15.2 1.0
C19 A:IL4402 4.8 25.8 1.0
CA A:SER115 5.0 18.6 1.0
C18 A:IL4402 5.0 26.3 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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