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Fluorine in PDB 8q0v: Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-((Methyl(Prop-2-Yn- 1-Yl)Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2, 4-Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-073)

Enzymatic activity of Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-((Methyl(Prop-2-Yn- 1-Yl)Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2, 4-Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-073)

All present enzymatic activity of Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-((Methyl(Prop-2-Yn- 1-Yl)Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2, 4-Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-073):
3.4.23.22;

Protein crystallography data

The structure of Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-((Methyl(Prop-2-Yn- 1-Yl)Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2, 4-Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-073), PDB code: 8q0v 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) 36.62 / 1.28
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.901, 72.654, 52.523, 90, 109.24, 90
R / Rfree (%) 14.9 / 17.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-((Methyl(Prop-2-Yn- 1-Yl)Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2, 4-Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-073) (pdb code 8q0v). 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(Prop-2-Yn- 1-Yl)Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2, 4-Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-073), PDB code: 8q0v:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8q0v

Go back to Fluorine Binding Sites List in 8q0v
Fluorine binding site 1 out of 3 in the Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-((Methyl(Prop-2-Yn- 1-Yl)Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2, 4-Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-073)


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(Prop-2-Yn- 1-Yl)Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2, 4-Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-073) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:22.0
occ:0.79
 F23 B:IKA401 0.0 22.0 0.8
C22 B:IKA401 1.4 20.2 0.8
F24 B:IKA401 2.2 20.2 0.8
F25 B:IKA401 2.2 21.6 0.8
C21 B:IKA401 2.4 18.5 0.8
C20 B:IKA401 2.8 17.9 0.8
CD1 B:PHE116 3.4 14.2 1.0
O B:SER115 3.5 16.6 1.0
CE1 B:PHE116 3.6 14.7 1.0
C26 B:IKA401 3.6 18.9 0.8
CB B:ASP119 3.9 21.2 1.0
CA B:PHE116 3.9 14.4 1.0
C B:SER115 4.0 15.4 1.0
N B:PHE116 4.1 14.3 1.0
CG B:PHE116 4.1 13.8 1.0
C19 B:IKA401 4.1 17.4 0.8
CD1 B:ILE122 4.2 15.1 1.0
O B:HOH646 4.2 14.4 1.0
OD2 B:ASP119 4.2 28.2 1.0
O B:HOH609 4.4 33.8 1.0
CG B:ASP119 4.4 26.1 1.0
CZ B:PHE116 4.6 14.9 1.0
CB B:PHE116 4.6 14.1 1.0
CB B:SER115 4.7 18.2 1.0
C27 B:IKA401 4.8 18.6 0.8
CD2 B:PHE116 5.0 14.4 1.0
CA B:SER115 5.0 17.0 1.0
C18 B:IKA401 5.0 17.9 0.8

Fluorine binding site 2 out of 3 in 8q0v

Go back to Fluorine Binding Sites List in 8q0v
Fluorine binding site 2 out of 3 in the Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-((Methyl(Prop-2-Yn- 1-Yl)Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2, 4-Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-073)


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(Prop-2-Yn- 1-Yl)Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2, 4-Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-073) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:20.2
occ:0.79
 F24 B:IKA401 0.0 20.2 0.8
C22 B:IKA401 1.4 20.2 0.8
F25 B:IKA401 2.2 21.6 0.8
F23 B:IKA401 2.2 22.0 0.8
C21 B:IKA401 2.3 18.5 0.8
C26 B:IKA401 2.8 18.9 0.8
CD1 B:PHE116 3.2 14.2 1.0
CB B:SER115 3.2 18.2 1.0
N B:PHE116 3.3 14.3 1.0
C B:SER115 3.3 15.4 1.0
CE1 B:PHE116 3.3 14.7 1.0
CG B:PHE116 3.4 13.8 1.0
OG B:SER83 3.5 18.0 0.6
C20 B:IKA401 3.5 17.9 0.8
O B:SER115 3.6 16.6 1.0
CZ B:PHE116 3.6 14.9 1.0
CD2 B:PHE116 3.6 14.4 1.0
CA B:PHE116 3.7 14.4 1.0
CE2 B:PHE116 3.8 15.3 1.0
CB B:SER83 3.8 17.0 0.6
CB B:SER83 3.8 16.9 0.4
CA B:SER115 3.9 17.0 1.0
OG B:SER83 4.0 17.3 0.4
CB B:PHE116 4.1 14.1 1.0
C27 B:IKA401 4.1 18.6 0.8
OD2 B:ASP81 4.3 21.3 1.0
OG B:SER115 4.5 19.7 1.0
C19 B:IKA401 4.6 17.4 0.8
N B:SER115 4.8 16.9 1.0
O B:HOH609 4.9 33.8 1.0
C18 B:IKA401 4.9 17.9 0.8
O B:HOH524 5.0 38.1 1.0

Fluorine binding site 3 out of 3 in 8q0v

Go back to Fluorine Binding Sites List in 8q0v
Fluorine binding site 3 out of 3 in the Endothiapepsin in Complex with Ligand (3R,5R)-3-(2-((Methyl(Prop-2-Yn- 1-Yl)Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2, 4-Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-073)


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(Prop-2-Yn- 1-Yl)Amino)Methyl)Thiazol-4-Yl)-5-(3-(4-(Trifluoromethyl)Phenyl)-1,2, 4-Oxadiazol-5-Yl)Pyrrolidin-3-Ol (Cbws-Se-073) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:21.6
occ:0.79
 F25 B:IKA401 0.0 21.6 0.8
C22 B:IKA401 1.4 20.2 0.8
F24 B:IKA401 2.2 20.2 0.8
F23 B:IKA401 2.2 22.0 0.8
C21 B:IKA401 2.3 18.5 0.8
C26 B:IKA401 3.0 18.9 0.8
C20 B:IKA401 3.4 17.9 0.8
CB B:SER115 3.6 18.2 1.0
O B:HOH609 3.7 33.8 1.0
O B:SER115 3.8 16.6 1.0
OD2 B:ASP81 4.0 21.3 1.0
C B:SER115 4.1 15.4 1.0
O B:HOH524 4.1 38.1 1.0
C27 B:IKA401 4.3 18.6 0.8
OG B:SER115 4.4 19.7 1.0
CA B:SER115 4.4 17.0 1.0
OG B:SER83 4.5 18.0 0.6
C19 B:IKA401 4.6 17.4 0.8
N B:PHE116 4.7 14.3 1.0
C18 B:IKA401 4.9 17.9 0.8

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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