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Sodium in PDB 5f00: Crystal Structure of Bace-1 in Complex with 5-[3-[(3-Chloro-8- Quinolyl)Amino]Phenyl]-5-Methyl-2,6-Dihydro-1,4-Oxazin-3-Amine

Enzymatic activity of Crystal Structure of Bace-1 in Complex with 5-[3-[(3-Chloro-8- Quinolyl)Amino]Phenyl]-5-Methyl-2,6-Dihydro-1,4-Oxazin-3-Amine

All present enzymatic activity of Crystal Structure of Bace-1 in Complex with 5-[3-[(3-Chloro-8- Quinolyl)Amino]Phenyl]-5-Methyl-2,6-Dihydro-1,4-Oxazin-3-Amine:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Bace-1 in Complex with 5-[3-[(3-Chloro-8- Quinolyl)Amino]Phenyl]-5-Methyl-2,6-Dihydro-1,4-Oxazin-3-Amine, PDB code: 5f00 was solved by D.Banner, J.Benz, M.Stihle, A.Kuglstatter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.82 / 1.95
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 103.504, 103.504, 169.212, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 26.3

Other elements in 5f00:

The structure of Crystal Structure of Bace-1 in Complex with 5-[3-[(3-Chloro-8- Quinolyl)Amino]Phenyl]-5-Methyl-2,6-Dihydro-1,4-Oxazin-3-Amine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Bace-1 in Complex with 5-[3-[(3-Chloro-8- Quinolyl)Amino]Phenyl]-5-Methyl-2,6-Dihydro-1,4-Oxazin-3-Amine (pdb code 5f00). 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-[3-[(3-Chloro-8- Quinolyl)Amino]Phenyl]-5-Methyl-2,6-Dihydro-1,4-Oxazin-3-Amine, PDB code: 5f00:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5f00

Go back to Sodium Binding Sites List in 5f00
Sodium binding site 1 out of 2 in the Crystal Structure of Bace-1 in Complex with 5-[3-[(3-Chloro-8- Quinolyl)Amino]Phenyl]-5-Methyl-2,6-Dihydro-1,4-Oxazin-3-Amine


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-[3-[(3-Chloro-8- Quinolyl)Amino]Phenyl]-5-Methyl-2,6-Dihydro-1,4-Oxazin-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:47.6
occ:1.00
 O A:HOH753 2.4 38.2 1.0
O A:HIS242 2.5 28.7 1.0
O A:HOH782 2.5 56.4 1.0
O A:TYR245 2.5 23.5 1.0
C A:HIS242 3.5 28.0 1.0
O A:HOH766 3.6 48.0 1.0
C A:TYR245 3.7 24.3 1.0
CE2 A:TYR245 4.1 19.9 1.0
CB A:HIS242 4.1 27.6 1.0
CD2 A:TYR245 4.1 22.2 1.0
CA A:HIS242 4.2 27.4 1.0
CZ A:TYR245 4.3 22.1 1.0
CG A:TYR245 4.4 22.9 1.0
O A:HOH668 4.5 47.0 1.0
CA A:THR246 4.5 24.8 1.0
N A:THR246 4.5 24.6 1.0
N A:SER243 4.6 28.5 1.0
CE1 A:TYR245 4.6 21.6 1.0
N A:TYR245 4.6 25.1 1.0
CD1 A:TYR245 4.6 20.2 1.0
CA A:TYR245 4.7 24.6 1.0
CA A:SER243 4.8 29.1 1.0
OH A:TYR245 4.9 22.0 1.0
O A:HOH635 4.9 45.7 1.0
O A:GLY247 5.0 23.8 1.0

Sodium binding site 2 out of 2 in 5f00

Go back to Sodium Binding Sites List in 5f00
Sodium binding site 2 out of 2 in the Crystal Structure of Bace-1 in Complex with 5-[3-[(3-Chloro-8- Quinolyl)Amino]Phenyl]-5-Methyl-2,6-Dihydro-1,4-Oxazin-3-Amine


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-[3-[(3-Chloro-8- Quinolyl)Amino]Phenyl]-5-Methyl-2,6-Dihydro-1,4-Oxazin-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:38.2
occ:1.00
 O A:HOH687 2.3 34.3 1.0
O A:HOH814 2.4 61.8 1.0
O A:THR205 2.4 35.4 1.0
O A:HOH816 2.4 48.0 1.0
O A:VAL202 2.5 30.5 1.0
C A:THR205 3.6 35.0 1.0
C A:VAL202 3.7 30.1 1.0
O A:HOH876 4.0 50.8 1.0
CA A:HIS206 4.2 34.6 1.0
CG1 A:VAL202 4.2 27.8 1.0
N A:HIS206 4.3 34.7 1.0
CA A:VAL202 4.4 28.7 1.0
O A:VAL207 4.5 26.7 1.0
C A:HIS206 4.5 33.0 1.0
N A:THR205 4.6 34.5 1.0
O A:LYS203 4.6 33.3 1.0
N A:LYS203 4.7 31.4 1.0
C A:LYS203 4.7 32.8 1.0
CA A:THR205 4.7 35.3 1.0
N A:VAL207 4.8 30.2 1.0
CA A:LYS203 4.9 32.6 1.0
CB A:VAL202 4.9 28.7 1.0
O A:HOH604 5.0 47.1 1.0

Reference:

B.Kuhn, W.Guba, J.Hert, D.Banner, C.Bissantz, S.Ceccarelli, W.Haap, M.Korner, A.Kuglstatter, C.Lerner, P.Mattei, W.Neidhart, E.Pinard, M.G.Rudolph, T.Schulz-Gasch, T.Woltering, M.Stahl. A Real-World Perspective on Molecular Design. J.Med.Chem. V. 59 4087 2016.
ISSN: ISSN 0022-2623
PubMed: 26878596
DOI: 10.1021/ACS.JMEDCHEM.5B01875
Page generated: Mon Oct 7 20:55:49 2024

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