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Fluorine in PDB 5ux4: Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-Dihydro-2H- Pyran-3-Yl)-1-Fluoro- 7-(2-Fluoropyridin-3-Yl)Spiro[Chromeno[2,3- C]Pyridine-5,4'-[1,3]Oxazol]-2'-Amine

Enzymatic activity of Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-Dihydro-2H- Pyran-3-Yl)-1-Fluoro- 7-(2-Fluoropyridin-3-Yl)Spiro[Chromeno[2,3- C]Pyridine-5,4'-[1,3]Oxazol]-2'-Amine

All present enzymatic activity of Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-Dihydro-2H- Pyran-3-Yl)-1-Fluoro- 7-(2-Fluoropyridin-3-Yl)Spiro[Chromeno[2,3- C]Pyridine-5,4'-[1,3]Oxazol]-2'-Amine:
3.4.23.5;

Protein crystallography data

The structure of Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-Dihydro-2H- Pyran-3-Yl)-1-Fluoro- 7-(2-Fluoropyridin-3-Yl)Spiro[Chromeno[2,3- C]Pyridine-5,4'-[1,3]Oxazol]-2'-Amine, PDB code: 5ux4 was solved by A.Sickmier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.68 / 2.81
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 136.514, 66.122, 99.555, 90.00, 99.53, 90.00
R / Rfree (%) 19.1 / 23.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-Dihydro-2H- Pyran-3-Yl)-1-Fluoro- 7-(2-Fluoropyridin-3-Yl)Spiro[Chromeno[2,3- C]Pyridine-5,4'-[1,3]Oxazol]-2'-Amine (pdb code 5ux4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-Dihydro-2H- Pyran-3-Yl)-1-Fluoro- 7-(2-Fluoropyridin-3-Yl)Spiro[Chromeno[2,3- C]Pyridine-5,4'-[1,3]Oxazol]-2'-Amine, PDB code: 5ux4:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5ux4

Go back to Fluorine Binding Sites List in 5ux4
Fluorine binding site 1 out of 4 in the Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-Dihydro-2H- Pyran-3-Yl)-1-Fluoro- 7-(2-Fluoropyridin-3-Yl)Spiro[Chromeno[2,3- C]Pyridine-5,4'-[1,3]Oxazol]-2'-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-Dihydro-2H- Pyran-3-Yl)-1-Fluoro- 7-(2-Fluoropyridin-3-Yl)Spiro[Chromeno[2,3- C]Pyridine-5,4'-[1,3]Oxazol]-2'-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:60.1
occ:1.00
 F33 A:3UT404 0.0 60.1 1.0
C11 A:3UT404 1.4 49.5 1.0
N12 A:3UT404 2.4 41.9 1.0
C8 A:3UT404 2.4 42.7 1.0
O7 A:3UT404 2.7 46.5 1.0
CD2 A:LEU83 3.3 53.2 1.0
CE1 A:TYR78 3.3 56.3 1.0
CD1 A:TYR78 3.4 52.7 1.0
C13 A:3UT404 3.6 37.9 1.0
C9 A:3UT404 3.7 34.9 1.0
CG2 A:ILE76 4.0 40.1 1.0
C4 A:3UT404 4.1 41.4 1.0
C14 A:3UT404 4.1 34.6 1.0
CZ A:TYR78 4.1 56.5 1.0
CG A:TYR78 4.2 45.5 1.0
NE1 A:TRP40 4.3 48.1 1.0
CZ2 A:TRP40 4.3 38.1 1.0
CD1 A:ILE129 4.4 39.9 1.0
CE2 A:TRP40 4.6 44.2 1.0
CZ A:PHE121 4.6 60.6 1.0
OH A:TYR78 4.8 57.8 1.0
C20 A:3UT404 4.8 39.3 1.0
CG A:LEU83 4.8 54.4 1.0
C32 A:3UT404 4.8 37.4 1.0
CE2 A:TYR78 4.8 44.8 1.0
CD2 A:TYR78 4.9 44.8 1.0
C3 A:3UT404 4.9 43.7 1.0
CB A:TYR78 5.0 41.9 1.0
C10 A:3UT404 5.0 46.5 1.0
CB A:ILE76 5.0 48.2 1.0
C5 A:3UT404 5.0 45.5 1.0

Fluorine binding site 2 out of 4 in 5ux4

Go back to Fluorine Binding Sites List in 5ux4
Fluorine binding site 2 out of 4 in the Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-Dihydro-2H- Pyran-3-Yl)-1-Fluoro- 7-(2-Fluoropyridin-3-Yl)Spiro[Chromeno[2,3- C]Pyridine-5,4'-[1,3]Oxazol]-2'-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-Dihydro-2H- Pyran-3-Yl)-1-Fluoro- 7-(2-Fluoropyridin-3-Yl)Spiro[Chromeno[2,3- C]Pyridine-5,4'-[1,3]Oxazol]-2'-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:42.0
occ:1.00
 F27 A:3UT404 0.0 42.0 1.0
C22 A:3UT404 1.4 38.4 1.0
N23 A:3UT404 2.3 44.0 1.0
C21 A:3UT404 2.4 33.4 1.0
C1 A:3UT404 2.8 43.8 1.0
O A:GLY228 2.9 38.8 1.0
C6 A:3UT404 3.0 44.1 1.0
CA A:GLY228 3.1 28.1 1.0
C A:GLY228 3.3 36.1 1.0
CG1 A:VAL31 3.4 35.0 1.0
C24 A:3UT404 3.5 25.2 1.0
C26 A:3UT404 3.6 31.4 1.0
C2 A:3UT404 3.9 37.5 1.0
CB A:VAL31 4.1 33.2 1.0
C25 A:3UT404 4.1 30.1 1.0
C5 A:3UT404 4.1 45.5 1.0
CG2 A:VAL31 4.2 35.0 1.0
N A:THR229 4.5 26.8 1.0
N18 A:3UT404 4.5 48.3 1.0
N A:GLY228 4.5 35.5 1.0
CZ A:PHE126 4.6 24.4 1.0
O A:THR227 4.7 28.1 1.0
C3 A:3UT404 4.8 43.7 1.0
CG A:ASP33 4.8 36.9 1.0
C4 A:3UT404 4.9 41.4 1.0
C10 A:3UT404 4.9 46.5 1.0
C17 A:3UT404 5.0 44.0 1.0
OD1 A:ASP33 5.0 45.9 1.0

Fluorine binding site 3 out of 4 in 5ux4

Go back to Fluorine Binding Sites List in 5ux4
Fluorine binding site 3 out of 4 in the Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-Dihydro-2H- Pyran-3-Yl)-1-Fluoro- 7-(2-Fluoropyridin-3-Yl)Spiro[Chromeno[2,3- C]Pyridine-5,4'-[1,3]Oxazol]-2'-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-Dihydro-2H- Pyran-3-Yl)-1-Fluoro- 7-(2-Fluoropyridin-3-Yl)Spiro[Chromeno[2,3- C]Pyridine-5,4'-[1,3]Oxazol]-2'-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:58.7
occ:1.00
 F33 B:3UT403 0.0 58.7 1.0
C11 B:3UT403 1.4 39.8 1.0
N12 B:3UT403 2.4 46.9 1.0
C8 B:3UT403 2.4 41.1 1.0
O7 B:3UT403 2.7 39.1 1.0
CE1 B:TYR78 3.2 57.3 1.0
CD2 B:LEU83 3.2 40.2 1.0
CD1 B:TYR78 3.5 59.4 1.0
C13 B:3UT403 3.6 39.0 1.0
C9 B:3UT403 3.7 40.5 1.0
CZ B:TYR78 3.9 65.9 1.0
NE1 B:TRP40 3.9 43.0 1.0
CG2 B:ILE76 4.0 43.8 1.0
CZ2 B:TRP40 4.1 31.6 1.0
C14 B:3UT403 4.1 40.5 1.0
C4 B:3UT403 4.2 43.1 1.0
CE2 B:TRP40 4.3 30.8 1.0
CD1 B:ILE129 4.3 42.3 1.0
OH B:TYR78 4.3 72.5 1.0
CG B:TYR78 4.4 66.7 1.0
CG B:LEU83 4.7 41.8 1.0
CE2 B:TYR78 4.7 57.5 1.0
CB B:ILE76 4.8 47.0 1.0
C20 B:3UT403 4.8 35.2 1.0
CD2 B:TYR78 4.9 60.0 1.0
C32 B:3UT403 4.9 48.1 1.0
C3 B:3UT403 4.9 44.3 1.0
C10 B:3UT403 5.0 44.3 1.0

Fluorine binding site 4 out of 4 in 5ux4

Go back to Fluorine Binding Sites List in 5ux4
Fluorine binding site 4 out of 4 in the Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-Dihydro-2H- Pyran-3-Yl)-1-Fluoro- 7-(2-Fluoropyridin-3-Yl)Spiro[Chromeno[2,3- C]Pyridine-5,4'-[1,3]Oxazol]-2'-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-Dihydro-2H- Pyran-3-Yl)-1-Fluoro- 7-(2-Fluoropyridin-3-Yl)Spiro[Chromeno[2,3- C]Pyridine-5,4'-[1,3]Oxazol]-2'-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:40.1
occ:1.00
 F27 B:3UT403 0.0 40.1 1.0
C22 B:3UT403 1.4 32.5 1.0
N23 B:3UT403 2.3 32.5 1.0
C21 B:3UT403 2.4 35.8 1.0
C1 B:3UT403 2.7 39.2 1.0
C6 B:3UT403 3.0 36.2 1.0
O B:GLY228 3.1 34.0 1.0
CA B:GLY228 3.3 29.9 1.0
CG1 B:VAL31 3.4 29.3 1.0
C24 B:3UT403 3.5 32.8 1.0
C B:GLY228 3.6 34.1 1.0
C26 B:3UT403 3.6 26.1 1.0
C2 B:3UT403 3.7 31.4 1.0
CB B:VAL31 3.9 29.4 1.0
C5 B:3UT403 4.1 45.8 1.0
C25 B:3UT403 4.1 36.1 1.0
CG2 B:VAL31 4.1 37.9 1.0
N18 B:3UT403 4.4 46.4 1.0
CZ B:PHE126 4.5 30.5 1.0
N B:GLY228 4.6 34.5 1.0
C3 B:3UT403 4.6 44.3 1.0
CG B:ASP33 4.7 43.3 1.0
OD2 B:ASP33 4.7 34.4 1.0
C4 B:3UT403 4.8 43.1 1.0
N B:THR229 4.8 22.9 1.0
C10 B:3UT403 4.9 44.3 1.0
OD1 B:ASP33 4.9 42.0 1.0
CB B:ASP33 4.9 30.8 1.0
O B:THR227 5.0 34.1 1.0
C17 B:3UT403 5.0 40.6 1.0

Reference:

J.D.Low, M.D.Bartberger, K.Chen, Y.Cheng, M.R.Fielden, V.Gore, D.Hickman, Q.Liu, E.Allen Sickmier, H.M.Vargas, J.Werner, R.D.White, D.A.Whittington, S.Wood, A.E.Minatti. Development of 2-Aminooxazoline 3-Azaxanthene Beta-Amyloid Cleaving Enzyme (Bace) Inhibitors with Improved Selectivity Against Cathepsin D. Medchemcomm V. 8 1196 2017.
ISSN: ISSN 2040-2503
PubMed: 30108829
DOI: 10.1039/C7MD00106A
Page generated: Thu Aug 1 15:52:16 2024

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