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Sodium in PDB 4j0y: Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5S)-2-Amino-5-Fluoro-4-Methyl-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,5S)-2-Amino-5-Fluoro-4-Methyl-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,5S)-2-Amino-5-Fluoro-4-Methyl-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,5S)-2-Amino-5-Fluoro-4-Methyl-5,6-Dihydro-4H- [1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j0y 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) 44.10 / 1.77
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.835, 101.835, 170.187, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 20

Other elements in 4j0y:

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

Fluorine (F) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5S)-2-Amino-5-Fluoro-4-Methyl-5,6-Dihydro-4H- [1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide (pdb code 4j0y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5S)-2-Amino-5-Fluoro-4-Methyl-5,6-Dihydro-4H- [1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j0y:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4j0y

Go back to Sodium Binding Sites List in 4j0y
Sodium binding site 1 out of 2 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5S)-2-Amino-5-Fluoro-4-Methyl-5,6-Dihydro-4H- [1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5S)-2-Amino-5-Fluoro-4-Methyl-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:Na501

b:44.9
occ:1.00
 O A:HOH930 2.0 57.9 1.0
O A:HOH675 2.3 36.7 1.0
O A:TYR245 2.4 24.4 1.0
O A:HIS242 2.5 28.5 1.0
C A:TYR245 3.4 25.3 1.0
C A:HIS242 3.6 28.7 1.0
CD2 A:TYR245 3.8 22.5 1.0
CE2 A:TYR245 3.8 24.0 1.0
CG A:TYR245 4.0 20.9 1.0
CZ A:TYR245 4.1 25.5 1.0
CA A:THR246 4.2 27.0 1.0
CA A:HIS242 4.2 26.9 1.0
CB A:HIS242 4.2 32.9 1.0
CD1 A:TYR245 4.2 21.1 1.0
N A:THR246 4.3 25.4 1.0
N A:TYR245 4.3 23.0 1.0
CE1 A:TYR245 4.3 25.1 1.0
CA A:TYR245 4.4 22.4 1.0
O A:HOH785 4.4 48.6 1.0
N A:SER243 4.7 29.2 1.0
O A:GLY247 4.7 28.4 1.0
OH A:TYR245 4.8 29.3 1.0
CB A:TYR245 4.8 20.4 1.0
O A:HOH776 4.8 43.4 1.0
C A:THR246 4.8 27.8 1.0
CA A:SER243 4.8 30.8 1.0

Sodium binding site 2 out of 2 in 4j0y

Go back to Sodium Binding Sites List in 4j0y
Sodium binding site 2 out of 2 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5S)-2-Amino-5-Fluoro-4-Methyl-5,6-Dihydro-4H- [1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5S)-2-Amino-5-Fluoro-4-Methyl-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:Na502

b:41.5
occ:1.00
 O A:VAL202 2.3 30.0 1.0
O A:HOH780 2.4 42.5 1.0
O A:HOH739 2.4 38.2 1.0
O A:THR205 2.4 37.9 1.0
O A:HOH786 2.4 53.7 1.0
O A:HOH907 2.5 47.9 1.0
C A:VAL202 3.5 30.3 1.0
C A:THR205 3.7 36.5 1.0
CG1 A:VAL202 4.2 29.1 1.0
CA A:HIS206 4.3 40.0 1.0
O A:LYS203 4.3 32.0 1.0
CA A:VAL202 4.3 28.2 1.0
O A:HOH919 4.3 47.4 1.0
N A:THR205 4.4 34.9 1.0
C A:LYS203 4.4 33.2 1.0
N A:HIS206 4.5 35.6 1.0
N A:LYS203 4.5 28.9 1.0
O A:VAL207 4.6 27.8 1.0
CA A:LYS203 4.6 34.0 1.0
C A:HIS206 4.7 33.8 1.0
CA A:THR205 4.7 34.6 1.0
N A:VAL207 4.9 30.9 1.0
CB A:VAL202 4.9 27.1 1.0
ND1 A:HIS206 4.9 59.5 1.0
O A:HOH764 4.9 47.8 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: Mon Oct 7 16:09:49 2024

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