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Sodium in PDB 4j1k: Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6S)-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,6S)-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,6S)-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,6S)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide, PDB code: 4j1k 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) 47.66 / 2.18
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.873, 102.873, 169.209, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 22.7

Other elements in 4j1k:

The structure of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6S)-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:

Fluorine (F) 5 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,5R,6S)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide (pdb code 4j1k). 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,5R,6S)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide, PDB code: 4j1k:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4j1k

Go back to Sodium Binding Sites List in 4j1k
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,5R,6S)-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 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,5R,6S)-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:Na501

b:65.9
occ:1.00
 O A:HIS242 2.6 44.6 1.0
O A:TYR245 2.7 40.9 1.0
O A:HOH1061 3.0 59.3 1.0
C A:HIS242 3.6 42.3 1.0
C A:TYR245 3.7 41.5 1.0
CE2 A:TYR245 3.8 37.8 1.0
CD2 A:TYR245 3.9 36.0 1.0
CB A:HIS242 4.0 53.9 1.0
CA A:HIS242 4.0 46.9 1.0
CZ A:TYR245 4.0 36.9 1.0
CG A:TYR245 4.3 36.2 1.0
CE1 A:TYR245 4.3 34.7 1.0
CA A:THR246 4.4 43.1 1.0
CD1 A:TYR245 4.5 34.7 1.0
N A:THR246 4.5 42.2 1.0
N A:TYR245 4.6 36.8 1.0
OH A:TYR245 4.6 42.8 1.0
CA A:TYR245 4.6 37.8 1.0
N A:SER243 4.7 42.1 1.0
O A:GLY247 4.9 37.5 1.0

Sodium binding site 2 out of 2 in 4j1k

Go back to Sodium Binding Sites List in 4j1k
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,5R,6S)-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 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,5R,6S)-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:Na502

b:64.1
occ:1.00
 O A:THR205 2.2 53.6 1.0
O A:HOH1091 2.4 48.4 1.0
O A:VAL202 2.5 49.7 1.0
O A:HOH1117 2.6 58.7 1.0
C A:THR205 3.5 53.5 1.0
C A:VAL202 3.7 43.5 1.0
CA A:HIS206 4.0 62.8 1.0
N A:HIS206 4.2 58.6 1.0
CG1 A:VAL202 4.2 37.5 1.0
N A:THR205 4.3 50.4 1.0
O A:LYS203 4.4 48.9 1.0
O A:VAL207 4.4 38.2 1.0
CA A:VAL202 4.4 40.1 1.0
C A:HIS206 4.5 56.3 1.0
CA A:THR205 4.5 49.9 1.0
C A:LYS203 4.6 47.7 1.0
N A:LYS203 4.7 44.0 1.0
N A:VAL207 4.7 52.1 1.0
CA A:LYS203 4.8 48.2 1.0
ND1 A:HIS206 4.8 93.8 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 16:10:53 2024

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