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Sodium in PDB 4j1i: Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-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,6R)-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,6R)-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,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide, PDB code: 4j1i 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) 47.61 / 2.05
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.781, 102.781, 169.040, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 22.6

Other elements in 4j1i:

The structure of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4R,5R,6R)-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,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide (pdb code 4j1i). 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,6R)-2-Amino-5-Fluoro-4-Methyl-6- Trifluoromethyl-5,6-Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]- Amide, PDB code: 4j1i:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4j1i

Go back to Sodium Binding Sites List in 4j1i
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,6R)-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,6R)-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:62.4
occ:1.00
 O A:HOH1080 2.2 49.5 1.0
O A:HIS242 2.4 38.3 1.0
O A:HOH1134 2.6 81.8 1.0
O A:TYR245 2.7 32.9 1.0
C A:HIS242 3.4 38.4 1.0
C A:TYR245 3.8 32.9 1.0
CA A:HIS242 3.9 39.8 1.0
CE2 A:TYR245 3.9 31.8 1.0
CB A:HIS242 3.9 46.6 1.0
CZ A:TYR245 4.0 31.5 1.0
CD2 A:TYR245 4.0 31.1 1.0
CE1 A:TYR245 4.2 30.8 1.0
CG A:TYR245 4.3 30.8 1.0
CD1 A:TYR245 4.3 30.9 1.0
CA A:THR246 4.4 36.0 1.0
N A:SER243 4.5 36.7 1.0
N A:THR246 4.5 34.3 1.0
N A:TYR245 4.5 32.5 1.0
OH A:TYR245 4.6 37.5 1.0
CA A:TYR245 4.7 32.0 1.0
CA A:SER243 4.9 40.7 1.0
O A:GLY247 4.9 35.8 1.0
CG A:HIS242 4.9 54.6 1.0

Sodium binding site 2 out of 2 in 4j1i

Go back to Sodium Binding Sites List in 4j1i
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,6R)-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,6R)-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:53.6
occ:1.00
 O A:HOH1088 2.3 39.6 1.0
O A:VAL202 2.3 43.9 1.0
O A:THR205 2.4 45.6 1.0
O A:HOH1089 2.5 54.1 1.0
C A:VAL202 3.5 39.1 1.0
C A:THR205 3.6 46.0 1.0
CG1 A:VAL202 4.0 35.1 1.0
CA A:HIS206 4.1 51.1 1.0
CA A:VAL202 4.3 37.2 1.0
O A:LYS203 4.3 42.4 1.0
N A:HIS206 4.3 48.8 1.0
N A:THR205 4.4 43.8 1.0
C A:LYS203 4.4 43.8 1.0
O A:VAL207 4.5 36.4 1.0
ND1 A:HIS206 4.5 78.7 1.0
N A:LYS203 4.5 41.1 1.0
CA A:LYS203 4.5 41.7 1.0
C A:HIS206 4.5 47.6 1.0
CA A:THR205 4.7 43.0 1.0
N A:VAL207 4.8 46.6 1.0
CB A:VAL202 4.9 33.8 1.0
O A:HOH1151 4.9 58.3 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 16:10:50 2024

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