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Sodium in PDB 4j1f: Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6S)-2-Amino-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-((4S,6S)-2-Amino-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-((4S,6S)-2-Amino-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-((4S,6S)-2-Amino-4-Methyl-6-Trifluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j1f 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) 47.97 / 2.25
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 103.495, 103.495, 170.358, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 24.9

Other elements in 4j1f:

The structure of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6S)-2-Amino-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) 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-((4S,6S)-2-Amino-4-Methyl-6-Trifluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide (pdb code 4j1f). 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-((4S,6S)-2-Amino-4-Methyl-6-Trifluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j1f:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4j1f

Go back to Sodium Binding Sites List in 4j1f
Sodium binding site 1 out of 2 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6S)-2-Amino-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-((4S,6S)-2-Amino-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:61.5
occ:1.00
 O A:HIS242 2.6 42.1 1.0
O A:HOH1062 2.9 57.0 1.0
O A:TYR245 3.0 38.2 1.0
C A:HIS242 3.5 41.5 1.0
CB A:HIS242 3.9 47.3 1.0
CE2 A:TYR245 4.0 32.9 1.0
CA A:HIS242 4.0 41.5 1.0
C A:TYR245 4.0 36.4 1.0
CZ A:TYR245 4.1 33.0 1.0
CD2 A:TYR245 4.2 33.6 1.0
CE1 A:TYR245 4.4 30.9 1.0
CG A:TYR245 4.5 31.8 1.0
OH A:TYR245 4.6 36.5 1.0
CD1 A:TYR245 4.6 30.8 1.0
N A:SER243 4.6 42.6 1.0
CA A:THR246 4.7 38.3 1.0
N A:THR246 4.8 34.4 1.0
N A:TYR245 4.9 35.5 1.0
O A:GLY247 4.9 36.7 1.0
CG A:HIS242 4.9 52.8 1.0
CA A:TYR245 5.0 33.9 1.0

Sodium binding site 2 out of 2 in 4j1f

Go back to Sodium Binding Sites List in 4j1f
Sodium binding site 2 out of 2 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6S)-2-Amino-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-((4S,6S)-2-Amino-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:59.1
occ:1.00
 O A:VAL202 2.6 43.2 1.0
O A:THR205 2.7 51.0 1.0
C A:VAL202 3.7 39.7 1.0
C A:THR205 3.9 50.0 1.0
CG1 A:VAL202 4.1 35.5 1.0
CA A:VAL202 4.4 35.6 1.0
CA A:HIS206 4.4 54.9 1.0
O A:VAL207 4.5 40.5 1.0
O A:LYS203 4.6 47.4 1.0
N A:HIS206 4.7 51.4 1.0
N A:LYS203 4.7 39.2 1.0
C A:LYS203 4.7 45.0 1.0
N A:THR205 4.8 47.0 1.0
C A:HIS206 4.8 48.0 1.0
CA A:LYS203 4.9 44.2 1.0
CB A:VAL202 4.9 35.9 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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