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Sodium in PDB 4j0p: Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((S)-2-Amino-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-Cyano-Pyridine-2- Carboxylic Acid [3-((S)-2-Amino-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-Cyano-Pyridine-2- Carboxylic Acid [3-((S)-2-Amino-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-Cyano-Pyridine-2- Carboxylic Acid [3-((S)-2-Amino-4-Methyl-5,6-Dihydro-4H-[1,3]Oxazin- 4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j0p 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) 49.08 / 1.97
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.537, 102.537, 169.795, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 23.1

Other elements in 4j0p:

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

Fluorine (F) 1 atom

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-4-Methyl-5,6-Dihydro-4H-[1,3]Oxazin- 4-Yl)-4-Fluoro-Phenyl]-Amide (pdb code 4j0p). 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-4-Methyl-5,6-Dihydro-4H-[1,3]Oxazin- 4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j0p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4j0p

Go back to Sodium Binding Sites List in 4j0p
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-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-Cyano-Pyridine-2- Carboxylic Acid [3-((S)-2-Amino-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:56.4
occ:1.00
 O A:TYR245 2.3 36.9 1.0
O A:HIS242 2.3 43.7 1.0
O A:HOH669 2.4 43.1 1.0
C A:TYR245 3.4 38.7 1.0
C A:HIS242 3.5 45.4 1.0
CD2 A:TYR245 3.9 33.5 1.0
CE2 A:TYR245 4.0 33.9 1.0
CG A:TYR245 4.1 32.7 1.0
CA A:THR246 4.2 38.1 1.0
CZ A:TYR245 4.2 37.8 1.0
CA A:HIS242 4.2 44.2 1.0
N A:TYR245 4.2 34.8 1.0
N A:THR246 4.2 39.0 1.0
CB A:HIS242 4.2 47.1 1.0
CA A:TYR245 4.3 35.5 1.0
CD1 A:TYR245 4.3 33.0 1.0
CE1 A:TYR245 4.4 34.1 1.0
O A:HOH751 4.5 64.4 1.0
N A:SER243 4.5 43.9 1.0
O A:HOH744 4.6 61.3 1.0
CA A:SER243 4.7 44.9 1.0
O A:GLY247 4.8 40.7 1.0
CB A:TYR245 4.8 31.4 1.0
C A:THR246 4.9 38.7 1.0
OH A:TYR245 4.9 38.7 1.0
C A:SER243 4.9 41.2 1.0

Sodium binding site 2 out of 2 in 4j0p

Go back to Sodium Binding Sites List in 4j0p
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-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-Cyano-Pyridine-2- Carboxylic Acid [3-((S)-2-Amino-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:62.6
occ:1.00
 O A:HOH726 2.1 48.5 1.0
O A:HOH752 2.3 62.6 1.0
O A:THR205 2.3 52.2 1.0
O A:HOH791 2.4 65.3 1.0
O A:VAL202 2.5 47.1 1.0
O A:HOH748 2.6 58.1 1.0
C A:THR205 3.5 50.0 1.0
C A:VAL202 3.6 43.5 1.0
CA A:HIS206 4.0 52.5 1.0
N A:HIS206 4.3 48.9 1.0
CG1 A:VAL202 4.3 45.9 1.0
CA A:VAL202 4.4 42.3 1.0
N A:THR205 4.4 46.0 1.0
C A:HIS206 4.5 47.9 1.0
O A:VAL207 4.5 40.9 1.0
O A:LYS203 4.6 49.9 1.0
CA A:THR205 4.6 48.7 1.0
N A:LYS203 4.6 43.7 1.0
C A:LYS203 4.7 49.3 1.0
N A:VAL207 4.7 43.8 1.0
CA A:LYS203 4.8 48.3 1.0
CB A:VAL202 5.0 41.3 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 16:09:49 2024

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