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Fluorine in PDB 4j1i: Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide

Enzymatic activity of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide

All present enzymatic activity of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide, PDB code: 4j1i was solved by A.Kuglstatter, M.Stihle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.61 / 2.05
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.781, 102.781, 169.040, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 22.6

Other elements in 4j1i:

The structure of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide (pdb code 4j1i). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide, PDB code: 4j1i:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 4j1i

Go back to Fluorine Binding Sites List in 4j1i
Fluorine binding site 1 out of 5 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide


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 Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:34.6
occ:1.00
 F13 A:1HH504 0.0 34.6 1.0
C10 A:1HH504 1.4 34.5 1.0
C9 A:1HH504 2.4 30.9 1.0
C14 A:1HH504 2.4 28.2 1.0
C1 A:1HH504 2.8 29.5 1.0
C12 A:1HH504 2.9 27.9 1.0
C2 A:1HH504 3.0 33.1 1.0
CE2 A:TYR132 3.1 51.4 1.0
CZ A:TYR132 3.3 48.2 1.0
CE1 A:PHE169 3.3 24.2 1.0
CD2 A:TYR132 3.5 43.1 1.0
C11 A:1HH504 3.6 27.7 1.0
C8 A:1HH504 3.6 31.8 1.0
CD1 A:PHE169 3.7 25.7 1.0
OH A:TYR132 3.8 58.0 1.0
CE1 A:TYR132 3.9 47.2 1.0
F18 A:1HH504 3.9 34.3 1.0
F17 A:1HH504 4.0 45.4 1.0
CG A:TYR132 4.0 42.8 1.0
F15 A:1HH504 4.0 51.1 1.0
C7 A:1HH504 4.1 31.6 1.0
O A:HOH1096 4.1 52.5 1.0
CD1 A:TYR132 4.1 45.0 1.0
C3 A:1HH504 4.2 37.4 1.0
C31 A:1HH504 4.3 41.4 1.0
N6 A:1HH504 4.3 28.6 1.0
CD1 A:ILE179 4.5 21.7 0.7
CZ A:PHE169 4.5 27.2 1.0
CB A:TYR132 5.0 43.9 1.0

Fluorine binding site 2 out of 5 in 4j1i

Go back to Fluorine Binding Sites List in 4j1i
Fluorine binding site 2 out of 5 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide


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 Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:51.1
occ:1.00
 F15 A:1HH504 0.0 51.1 1.0
C31 A:1HH504 1.4 41.4 1.0
F16 A:1HH504 2.2 45.3 1.0
F17 A:1HH504 2.3 45.4 1.0
C3 A:1HH504 2.3 37.4 1.0
C2 A:1HH504 2.8 33.1 1.0
O A:HOH1087 3.5 59.3 1.0
O4 A:1HH504 3.6 32.1 1.0
CB A:TYR132 3.6 43.9 1.0
F18 A:1HH504 3.7 34.3 1.0
CG A:TYR132 3.8 42.8 1.0
CD1 A:TYR132 3.8 45.0 1.0
F13 A:1HH504 4.0 34.6 1.0
C1 A:1HH504 4.1 29.5 1.0
C10 A:1HH504 4.2 34.5 1.0
C14 A:1HH504 4.2 28.2 1.0
CD2 A:TYR132 4.6 43.1 1.0
CE1 A:TYR132 4.6 47.2 1.0
C5 A:1HH504 4.6 30.4 1.0
O A:HOH1096 4.8 52.5 1.0
N6 A:1HH504 4.9 28.6 1.0
CA A:TYR132 4.9 48.5 1.0
C11 A:1HH504 5.0 27.7 1.0
C9 A:1HH504 5.0 30.9 1.0

Fluorine binding site 3 out of 5 in 4j1i

Go back to Fluorine Binding Sites List in 4j1i
Fluorine binding site 3 out of 5 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide


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 Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:45.3
occ:1.00
 F16 A:1HH504 0.0 45.3 1.0
C31 A:1HH504 1.4 41.4 1.0
F17 A:1HH504 2.1 45.4 1.0
F15 A:1HH504 2.2 51.1 1.0
C3 A:1HH504 2.4 37.4 1.0
O4 A:1HH504 2.8 32.1 1.0
O A:HOH1058 3.5 47.7 1.0
C2 A:1HH504 3.7 33.1 1.0
O A:HOH1135 4.1 39.6 1.0
C5 A:1HH504 4.1 30.4 1.0
F18 A:1HH504 4.5 34.3 1.0
O A:HOH1087 4.7 59.3 1.0
O A:HOH1140 4.7 47.7 1.0
C1 A:1HH504 4.7 29.5 1.0
OG1 A:THR292 4.8 35.9 1.0
C14 A:1HH504 4.8 28.2 1.0
N6 A:1HH504 4.9 28.6 1.0
O A:HOH1180 4.9 55.5 1.0
N19 A:1HH504 4.9 28.4 1.0

Fluorine binding site 4 out of 5 in 4j1i

Go back to Fluorine Binding Sites List in 4j1i
Fluorine binding site 4 out of 5 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide


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 Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:45.4
occ:1.00
 F17 A:1HH504 0.0 45.4 1.0
C31 A:1HH504 1.4 41.4 1.0
F16 A:1HH504 2.1 45.3 1.0
F15 A:1HH504 2.3 51.1 1.0
C3 A:1HH504 2.4 37.4 1.0
O4 A:1HH504 2.8 32.1 1.0
C14 A:1HH504 3.1 28.2 1.0
C2 A:1HH504 3.1 33.1 1.0
C11 A:1HH504 3.2 27.7 1.0
O A:HOH1135 3.3 39.6 1.0
C10 A:1HH504 3.4 34.5 1.0
C1 A:1HH504 3.5 29.5 1.0
C7 A:1HH504 3.7 31.6 1.0
C5 A:1HH504 3.7 30.4 1.0
C9 A:1HH504 3.8 30.9 1.0
F13 A:1HH504 4.0 34.6 1.0
C8 A:1HH504 4.0 31.8 1.0
N6 A:1HH504 4.0 28.6 1.0
F18 A:1HH504 4.3 34.3 1.0
O A:GLY291 4.5 27.8 1.0
N20 A:1HH504 4.5 30.6 1.0
O A:HOH1087 4.6 59.3 1.0
O A:HOH1096 4.7 52.5 1.0
N19 A:1HH504 4.8 28.4 1.0
C12 A:1HH504 4.9 27.9 1.0

Fluorine binding site 5 out of 5 in 4j1i

Go back to Fluorine Binding Sites List in 4j1i
Fluorine binding site 5 out of 5 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:34.3
occ:1.00
 F18 A:1HH504 0.0 34.3 1.0
C2 A:1HH504 1.4 33.1 1.0
C3 A:1HH504 2.3 37.4 1.0
C1 A:1HH504 2.3 29.5 1.0
C12 A:1HH504 2.6 27.9 1.0
N6 A:1HH504 2.9 28.6 1.0
O4 A:1HH504 3.1 32.1 1.0
CE1 A:TYR132 3.1 47.2 1.0
C5 A:1HH504 3.1 30.4 1.0
CD1 A:TYR132 3.5 45.0 1.0
C31 A:1HH504 3.5 41.4 1.0
O A:HOH1128 3.5 52.0 1.0
F15 A:1HH504 3.7 51.1 1.0
C14 A:1HH504 3.7 28.2 1.0
O A:HOH1173 3.8 66.6 1.0
O A:HOH1180 3.9 55.5 1.0
CZ A:TYR132 3.9 48.2 1.0
F13 A:1HH504 3.9 34.6 1.0
N19 A:1HH504 4.3 28.4 1.0
CB A:SER96 4.3 24.0 1.0
C10 A:1HH504 4.3 34.5 1.0
OH A:TYR132 4.3 58.0 1.0
F17 A:1HH504 4.3 45.4 1.0
CG A:TYR132 4.5 42.8 1.0
F16 A:1HH504 4.5 45.3 1.0
O A:GLY95 4.6 24.5 1.0
OD2 A:ASP93 4.6 25.8 1.0
C11 A:1HH504 4.7 27.7 1.0
CE2 A:TYR132 4.9 51.4 1.0
O A:HOH1131 4.9 43.9 1.0
OG A:SER96 4.9 24.1 1.0

Reference:

H.Hilpert, W.Guba, T.J.Woltering, W.Wostl, E.Pinard, H.Mauser, A.V.Mayweg, M.Rogers-Evans, R.Humm, D.Krummenacher, T.Muser, C.Schnider, H.Jacobsen, L.Ozmen, A.Bergadano, D.W.Banner, R.Hochstrasser, A.Kuglstatter, P.David-Pierson, H.Fischer, A.Polara, R.Narquizian. Beta-Secretase (BACE1) Inhibitors with High in Vivo Efficacy Suitable For Clinical Evaluation in Alzheimer S Disease J.Med.Chem. V. 56 3980 2013.
ISSN: ISSN 0022-2623
PubMed: 23590342
DOI: 10.1021/JM400225M
Page generated: Thu Aug 1 02:45:33 2024

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