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 / R_free (%)*	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

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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

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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

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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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