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Sodium in PDB 4j1c: Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((S)-2-Amino-5,5-Difluoro-4-Fluoromethyl-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-5,5-Difluoro-4-Fluoromethyl-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-5,5-Difluoro-4-Fluoromethyl-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-5,5-Difluoro-4-Fluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j1c 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) 49.04 / 2.01
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.452, 102.452, 169.488, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 21.7

Other elements in 4j1c:

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

Fluorine (F) 4 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-((S)-2-Amino-5,5-Difluoro-4-Fluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide (pdb code 4j1c). 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-((S)-2-Amino-5,5-Difluoro-4-Fluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j1c:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4j1c

Go back to Sodium Binding Sites List in 4j1c
Sodium binding site 1 out of 2 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((S)-2-Amino-5,5-Difluoro-4-Fluoromethyl-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-((S)-2-Amino-5,5-Difluoro-4-Fluoromethyl-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:70.8
occ:1.00
 O A:HOH672 2.4 56.5 1.0
O A:TYR245 2.5 45.8 1.0
O A:HIS242 2.5 53.1 1.0
O A:HOH801 2.5 80.2 1.0
O A:HOH745 3.1 86.1 1.0
C A:HIS242 3.6 49.5 1.0
C A:TYR245 3.6 45.1 1.0
CD2 A:TYR245 4.0 39.2 1.0
CE2 A:TYR245 4.1 41.3 1.0
CA A:HIS242 4.2 49.0 1.0
CB A:HIS242 4.2 54.4 1.0
CG A:TYR245 4.2 39.1 1.0
CA A:THR246 4.3 46.0 1.0
CZ A:TYR245 4.4 41.8 1.0
N A:THR246 4.4 44.3 1.0
N A:TYR245 4.5 41.4 1.0
CD1 A:TYR245 4.5 40.0 1.0
CA A:TYR245 4.5 41.6 1.0
CE1 A:TYR245 4.5 42.0 1.0
O A:HOH761 4.5 64.8 1.0
N A:SER243 4.6 54.0 1.0
CA A:SER243 4.8 54.1 1.0
O A:GLY247 4.8 46.6 1.0
C A:THR246 4.9 45.2 1.0
CB A:TYR245 5.0 39.2 1.0
OH A:TYR245 5.0 46.4 1.0

Sodium binding site 2 out of 2 in 4j1c

Go back to Sodium Binding Sites List in 4j1c
Sodium binding site 2 out of 2 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((S)-2-Amino-5,5-Difluoro-4-Fluoromethyl-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-((S)-2-Amino-5,5-Difluoro-4-Fluoromethyl-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:HOH793 2.2 81.7 1.0
O A:THR205 2.2 64.4 1.0
O A:HOH733 2.3 60.9 1.0
O A:VAL202 2.4 56.4 1.0
O A:HOH767 2.7 72.4 1.0
C A:THR205 3.5 66.7 1.0
C A:VAL202 3.6 54.4 1.0
CA A:HIS206 4.0 68.5 1.0
CG1 A:VAL202 4.1 47.4 1.0
N A:HIS206 4.2 64.6 1.0
N A:THR205 4.3 60.8 1.0
O A:LYS203 4.3 63.0 1.0
CA A:VAL202 4.4 47.7 1.0
O A:VAL207 4.4 48.7 1.0
C A:HIS206 4.4 63.2 1.0
C A:LYS203 4.5 59.5 1.0
N A:LYS203 4.5 54.7 1.0
CA A:THR205 4.6 63.7 1.0
CA A:LYS203 4.6 60.2 1.0
N A:VAL207 4.8 57.5 1.0
CB A:VAL202 4.9 45.4 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 16:10:35 2024

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