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Fluorine in PDB 4j17: Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((S)-2-Amino-4-Difluoromethyl-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-((S)-2-Amino-4-Difluoromethyl-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-((S)-2-Amino-4-Difluoromethyl-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-((S)-2-Amino-4-Difluoromethyl-5,6-Dihydro-4H-[1, 3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j17 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) 48.99 / 1.81
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.307, 102.307, 170.080, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 20.8

Other elements in 4j17:

The structure of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((S)-2-Amino-4-Difluoromethyl-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-((S)-2-Amino-4-Difluoromethyl-5,6-Dihydro-4H-[1, 3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide (pdb code 4j17). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((S)-2-Amino-4-Difluoromethyl-5,6-Dihydro-4H-[1, 3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j17:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4j17

Go back to Fluorine Binding Sites List in 4j17
Fluorine binding site 1 out of 3 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((S)-2-Amino-4-Difluoromethyl-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-((S)-2-Amino-4-Difluoromethyl-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:28.8
occ:1.00
 F18 A:1HQ504 0.0 28.8 1.0
C15 A:1HQ504 1.4 30.4 1.0
C16 A:1HQ504 2.4 26.7 1.0
C14 A:1HQ504 2.5 28.6 1.0
C25 A:1HQ504 2.8 28.6 1.0
C19 A:1HQ504 2.9 26.2 1.0
CE2 A:TYR132 3.1 40.3 1.0
C20 A:1HQ504 3.2 26.2 1.0
CE1 A:PHE169 3.3 25.4 1.0
CD2 A:TYR132 3.4 42.0 1.0
F26 A:1HQ504 3.4 31.9 1.0
CD1 A:PHE169 3.5 26.9 1.0
O A:HOH797 3.6 43.3 1.0
CZ A:TYR132 3.6 41.5 1.0
C17 A:1HQ504 3.7 24.9 1.0
C13 A:1HQ504 3.7 29.0 1.0
F27 A:1HQ504 4.0 31.3 1.0
OH A:TYR132 4.1 53.3 1.0
CG A:TYR132 4.1 38.4 1.0
C12 A:1HQ504 4.2 24.9 1.0
CD1 A:ILE179 4.3 29.0 1.0
C21 A:1HQ504 4.3 27.8 1.0
N24 A:1HQ504 4.3 24.4 1.0
CE1 A:TYR132 4.3 40.2 1.0
CD1 A:TYR132 4.5 42.2 1.0
CZ A:PHE169 4.5 27.4 1.0
CG A:PHE169 4.8 25.0 1.0
CB A:TYR132 5.0 39.3 1.0

Fluorine binding site 2 out of 3 in 4j17

Go back to Fluorine Binding Sites List in 4j17
Fluorine binding site 2 out of 3 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((S)-2-Amino-4-Difluoromethyl-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-((S)-2-Amino-4-Difluoromethyl-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:31.9
occ:1.00
 F26 A:1HQ504 0.0 31.9 1.0
C25 A:1HQ504 1.4 28.6 1.0
F27 A:1HQ504 2.2 31.3 1.0
C19 A:1HQ504 2.4 26.2 1.0
N24 A:1HQ504 2.8 24.4 1.0
OD2 A:ASP93 2.8 26.3 1.0
C16 A:1HQ504 2.9 26.7 1.0
CD1 A:ILE179 3.3 29.0 1.0
F18 A:1HQ504 3.4 28.8 1.0
C15 A:1HQ504 3.4 30.4 1.0
OG A:SER96 3.5 24.7 1.0
C20 A:1HQ504 3.7 26.2 1.0
C17 A:1HQ504 3.7 24.9 1.0
OH A:TYR132 3.8 53.3 1.0
CG2 A:ILE179 3.8 22.0 1.0
CB A:SER96 4.0 22.0 1.0
C23 A:1HQ504 4.1 26.9 1.0
CG A:ASP93 4.1 23.5 1.0
O A:HOH608 4.2 23.6 1.0
CZ A:TYR132 4.2 41.5 1.0
CG1 A:ILE179 4.4 24.9 1.0
CB A:ILE179 4.4 22.2 1.0
C14 A:1HQ504 4.6 28.6 1.0
CE1 A:PHE169 4.6 25.4 1.0
CE1 A:TYR132 4.7 40.2 1.0
CE2 A:TYR132 4.8 40.3 1.0
C12 A:1HQ504 4.8 24.9 1.0
CB A:ASP93 4.9 21.1 1.0
C21 A:1HQ504 4.9 27.8 1.0
O22 A:1HQ504 4.9 29.2 1.0
OD1 A:ASP93 4.9 24.2 1.0
N28 A:1HQ504 4.9 23.6 1.0

Fluorine binding site 3 out of 3 in 4j17

Go back to Fluorine Binding Sites List in 4j17
Fluorine binding site 3 out of 3 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((S)-2-Amino-4-Difluoromethyl-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-((S)-2-Amino-4-Difluoromethyl-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:31.3
occ:1.00
 F27 A:1HQ504 0.0 31.3 1.0
C25 A:1HQ504 1.4 28.6 1.0
F26 A:1HQ504 2.2 31.9 1.0
C19 A:1HQ504 2.3 26.2 1.0
N24 A:1HQ504 2.7 24.4 1.0
C20 A:1HQ504 2.8 26.2 1.0
CE1 A:TYR132 3.2 40.2 1.0
CB A:SER96 3.2 22.0 1.0
CZ A:TYR132 3.4 41.5 1.0
OH A:TYR132 3.5 53.3 1.0
C23 A:1HQ504 3.5 26.9 1.0
OD2 A:ASP93 3.6 26.3 1.0
OG A:SER96 3.7 24.7 1.0
C16 A:1HQ504 3.7 26.7 1.0
O A:HOH802 3.8 41.3 1.0
F18 A:1HQ504 4.0 28.8 1.0
CD1 A:TYR132 4.0 42.2 1.0
O22 A:1HQ504 4.1 29.2 1.0
C21 A:1HQ504 4.1 27.8 1.0
CE2 A:TYR132 4.4 40.3 1.0
C15 A:1HQ504 4.4 30.4 1.0
N28 A:1HQ504 4.5 23.6 1.0
CA A:SER96 4.6 23.0 1.0
O A:HOH608 4.7 23.6 1.0
C17 A:1HQ504 4.7 24.9 1.0
O A:GLY95 4.8 21.9 1.0
CG A:ASP93 4.8 23.5 1.0
CG A:TYR132 4.8 38.4 1.0
CD2 A:TYR132 5.0 42.0 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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