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Sodium in PDB 4j0t: Crystal Structure of Bace-1 in Complex with 5-Ethoxy-Pyridine-2- Carboxylic Acid [3-((R)-2-Amino-5,5-Difluoro-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-Ethoxy-Pyridine-2- Carboxylic Acid [3-((R)-2-Amino-5,5-Difluoro-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-Ethoxy-Pyridine-2- Carboxylic Acid [3-((R)-2-Amino-5,5-Difluoro-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-Ethoxy-Pyridine-2- Carboxylic Acid [3-((R)-2-Amino-5,5-Difluoro-4-Methyl-5,6-Dihydro-4H- [1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j0t 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) 47.86 / 2.05
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.221, 102.221, 170.658, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 21

Other elements in 4j0t:

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

Fluorine (F) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Bace-1 in Complex with 5-Ethoxy-Pyridine-2- Carboxylic Acid [3-((R)-2-Amino-5,5-Difluoro-4-Methyl-5,6-Dihydro-4H- [1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide (pdb code 4j0t). 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-Ethoxy-Pyridine-2- Carboxylic Acid [3-((R)-2-Amino-5,5-Difluoro-4-Methyl-5,6-Dihydro-4H- [1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j0t:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4j0t

Go back to Sodium Binding Sites List in 4j0t
Sodium binding site 1 out of 2 in the Crystal Structure of Bace-1 in Complex with 5-Ethoxy-Pyridine-2- Carboxylic Acid [3-((R)-2-Amino-5,5-Difluoro-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-Ethoxy-Pyridine-2- Carboxylic Acid [3-((R)-2-Amino-5,5-Difluoro-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:38.7
occ:1.00
 O A:HOH672 2.4 29.7 1.0
O A:TYR245 2.5 30.0 1.0
O A:HIS242 2.6 32.5 1.0
O A:HOH744 3.2 53.6 1.0
C A:TYR245 3.6 30.2 1.0
C A:HIS242 3.7 34.0 1.0
CE2 A:TYR245 3.8 27.5 1.0
CD2 A:TYR245 3.8 25.4 1.0
CZ A:TYR245 4.0 31.1 1.0
CG A:TYR245 4.1 26.1 1.0
CB A:HIS242 4.2 35.7 1.0
CA A:HIS242 4.2 33.9 1.0
CE1 A:TYR245 4.3 28.8 1.0
CD1 A:TYR245 4.3 26.3 1.0
CA A:THR246 4.3 31.1 1.0
N A:THR246 4.4 30.8 1.0
N A:TYR245 4.5 29.1 1.0
CA A:TYR245 4.5 28.0 1.0
OH A:TYR245 4.7 34.1 1.0
O A:GLY247 4.7 34.5 1.0
O A:HOH766 4.7 49.5 1.0
N A:SER243 4.7 34.9 1.0
O A:HOH759 4.8 56.5 1.0
C A:THR246 4.9 30.2 1.0
CB A:TYR245 5.0 23.3 1.0
CA A:SER243 5.0 34.6 1.0

Sodium binding site 2 out of 2 in 4j0t

Go back to Sodium Binding Sites List in 4j0t
Sodium binding site 2 out of 2 in the Crystal Structure of Bace-1 in Complex with 5-Ethoxy-Pyridine-2- Carboxylic Acid [3-((R)-2-Amino-5,5-Difluoro-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-Ethoxy-Pyridine-2- Carboxylic Acid [3-((R)-2-Amino-5,5-Difluoro-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:69.5
occ:1.00
 O A:HOH767 2.2 48.2 1.0
O A:THR205 2.9 45.9 1.0
O A:LYS203 3.1 39.7 1.0
O A:VAL202 3.1 39.1 1.0
C A:LYS203 3.7 39.5 1.0
C A:THR205 4.0 43.0 1.0
CA A:LYS203 4.2 39.5 1.0
O A:HOH731 4.2 40.5 1.0
N A:THR205 4.2 38.1 1.0
C A:VAL202 4.3 35.5 1.0
N A:GLN204 4.6 37.5 1.0
C A:GLN204 4.7 42.5 1.0
CA A:THR205 4.7 41.9 1.0
N A:LYS203 4.7 37.7 1.0
N A:HIS206 5.0 43.0 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: Mon Oct 7 16:09:49 2024

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