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Fluorine in PDB 8q13: Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(2-Amino-4- (Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2- Yn-1-Yl)Amino)Methyl)Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-168)

Enzymatic activity of Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(2-Amino-4- (Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2- Yn-1-Yl)Amino)Methyl)Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-168)

All present enzymatic activity of Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(2-Amino-4- (Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2- Yn-1-Yl)Amino)Methyl)Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-168):
3.4.23.22;

Protein crystallography data

The structure of Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(2-Amino-4- (Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2- Yn-1-Yl)Amino)Methyl)Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-168), PDB code: 8q13 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) 36.60 / 1.26
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.875, 72.688, 52.502, 90, 109.24, 90
R / Rfree (%) 14.7 / 17.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(2-Amino-4- (Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2- Yn-1-Yl)Amino)Methyl)Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-168) (pdb code 8q13). 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)-5-(3-(2-Amino-4- (Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2- Yn-1-Yl)Amino)Methyl)Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-168), PDB code: 8q13:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8q13

Go back to Fluorine Binding Sites List in 8q13
Fluorine binding site 1 out of 3 in the Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(2-Amino-4- (Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2- Yn-1-Yl)Amino)Methyl)Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-168)


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-(2-Amino-4- (Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2- Yn-1-Yl)Amino)Methyl)Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-168) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F409

b:31.3
occ:0.66
 F30 A:IK5409 0.0 31.3 0.7
C29 A:IK5409 1.4 30.4 0.7
F32 A:IK5409 2.2 29.8 0.7
F31 A:IK5409 2.2 32.6 0.7
C25 A:IK5409 2.4 29.1 0.7
C26 A:IK5409 3.1 28.2 0.7
C24 A:IK5409 3.3 28.7 0.7
O A:HOH561 3.5 36.8 1.0
O A:SER115 3.8 17.6 1.0
CB A:SER115 3.8 21.3 1.0
C A:SER115 4.2 17.1 1.0
C27 A:IK5409 4.3 28.5 0.7
OD2 A:ASP81 4.5 29.3 1.0
C23 A:IK5409 4.5 28.5 0.7
CA A:SER115 4.5 18.6 1.0
OG A:SER115 4.6 23.6 1.0
OD2 A:ASP119 4.7 31.1 1.0
N A:PHE116 4.9 15.3 1.0
CB A:ASP119 4.9 20.9 1.0
OG A:SER83 4.9 17.9 0.3
C22 A:IK5409 4.9 28.2 0.7

Fluorine binding site 2 out of 3 in 8q13

Go back to Fluorine Binding Sites List in 8q13
Fluorine binding site 2 out of 3 in the Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(2-Amino-4- (Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2- Yn-1-Yl)Amino)Methyl)Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-168)


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-(2-Amino-4- (Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2- Yn-1-Yl)Amino)Methyl)Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-168) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F409

b:32.6
occ:0.66
 F31 A:IK5409 0.0 32.6 0.7
C29 A:IK5409 1.4 30.4 0.7
F32 A:IK5409 2.2 29.8 0.7
F30 A:IK5409 2.2 31.3 0.7
C25 A:IK5409 2.4 29.1 0.7
C24 A:IK5409 2.7 28.7 0.7
O A:SER115 3.5 17.6 1.0
CD1 A:PHE116 3.6 15.2 1.0
C26 A:IK5409 3.6 28.2 0.7
CB A:ASP119 3.7 20.9 1.0
OD2 A:ASP119 3.8 31.1 1.0
CE1 A:PHE116 3.9 16.1 1.0
C A:SER115 4.0 17.1 1.0
CA A:PHE116 4.1 14.3 1.0
O A:HOH664 4.1 15.5 1.0
C23 A:IK5409 4.1 28.5 0.7
CD1 A:ILE122 4.1 16.4 1.0
CG A:ASP119 4.2 27.1 1.0
O A:HOH561 4.2 36.8 1.0
N A:PHE116 4.3 15.3 1.0
CG A:PHE116 4.4 14.7 1.0
C27 A:IK5409 4.8 28.5 0.7
CB A:PHE116 4.8 14.2 1.0
CB A:SER115 4.9 21.3 1.0
CZ A:PHE116 4.9 16.1 1.0
C22 A:IK5409 4.9 28.2 0.7
CB A:ILE122 5.0 12.9 1.0

Fluorine binding site 3 out of 3 in 8q13

Go back to Fluorine Binding Sites List in 8q13
Fluorine binding site 3 out of 3 in the Endothiapepsin in Complex with Ligand (3R,5R)-5-(3-(2-Amino-4- (Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2- Yn-1-Yl)Amino)Methyl)Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-168)


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)-5-(3-(2-Amino-4- (Trifluoromethyl)Phenyl)-1,2,4-Oxadiazol-5-Yl)-3-(2-((Methyl(Prop-2- Yn-1-Yl)Amino)Methyl)Thiazol-4-Yl)Pyrrolidin-3-Ol (Cbws-Se-168) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F409

b:29.8
occ:0.66
 F32 A:IK5409 0.0 29.8 0.7
C29 A:IK5409 1.4 30.4 0.7
F30 A:IK5409 2.2 31.3 0.7
F31 A:IK5409 2.2 32.6 0.7
C25 A:IK5409 2.3 29.1 0.7
C26 A:IK5409 2.8 28.2 0.7
C A:SER115 3.1 17.1 1.0
CB A:SER115 3.1 21.3 1.0
N A:PHE116 3.2 15.3 1.0
O A:SER115 3.2 17.6 1.0
CD1 A:PHE116 3.3 15.2 1.0
CE1 A:PHE116 3.5 16.1 1.0
C24 A:IK5409 3.5 28.7 0.7
CG A:PHE116 3.6 14.7 1.0
CA A:PHE116 3.6 14.3 1.0
CA A:SER115 3.7 18.6 1.0
OG A:SER83 3.8 17.9 0.3
CZ A:PHE116 3.9 16.1 1.0
CD2 A:PHE116 4.0 15.1 1.0
C27 A:IK5409 4.1 28.5 0.7
CE2 A:PHE116 4.2 16.4 1.0
CB A:PHE116 4.2 14.2 1.0
CB A:SER83 4.2 18.4 0.3
CB A:SER83 4.2 19.9 0.7
OG A:SER83 4.3 20.5 0.7
OG A:SER115 4.4 23.6 1.0
O A:HOH561 4.5 36.8 1.0
OD2 A:ASP81 4.5 29.3 1.0
C23 A:IK5409 4.7 28.5 0.7
N A:SER115 4.7 18.1 1.0
C22 A:IK5409 4.9 28.2 0.7
C A:PHE116 5.0 14.8 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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