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Sodium in PDB 5ezz: Crystal Structure of Bace-1 in Complex with (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine

Enzymatic activity of Crystal Structure of Bace-1 in Complex with (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine

All present enzymatic activity of Crystal Structure of Bace-1 in Complex with (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Bace-1 in Complex with (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine, PDB code: 5ezz 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) 47.84 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.670, 102.670, 170.120, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / 24

Other elements in 5ezz:

The structure of Crystal Structure of Bace-1 in Complex with (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Bace-1 in Complex with (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine (pdb code 5ezz). 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 (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine, PDB code: 5ezz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5ezz

Go back to Sodium Binding Sites List in 5ezz
Sodium binding site 1 out of 2 in the Crystal Structure of Bace-1 in Complex with (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- 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 (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:41.6
occ:1.00
 O A:VAL202 2.2 40.9 1.0
O A:THR205 2.3 40.9 1.0
O A:HOH698 2.4 45.8 1.0
O A:HOH823 3.0 56.1 1.0
C A:VAL202 3.4 40.6 1.0
C A:THR205 3.5 40.7 1.0
O A:LYS203 4.2 42.0 1.0
N A:THR205 4.3 40.1 1.0
O A:HOH851 4.3 46.9 1.0
C A:LYS203 4.3 41.0 1.0
CA A:VAL202 4.3 40.0 1.0
CG1 A:VAL202 4.3 40.7 1.0
N A:LYS203 4.3 41.0 1.0
CA A:HIS206 4.4 41.9 1.0
N A:HIS206 4.4 40.8 1.0
CA A:LYS203 4.4 41.4 1.0
CA A:THR205 4.5 40.7 1.0
O A:VAL207 4.7 34.6 1.0
N A:GLN204 4.8 39.9 1.0
C A:HIS206 4.9 40.8 1.0
CB A:VAL202 5.0 39.9 1.0

Sodium binding site 2 out of 2 in 5ezz

Go back to Sodium Binding Sites List in 5ezz
Sodium binding site 2 out of 2 in the Crystal Structure of Bace-1 in Complex with (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- 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 (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:37.9
occ:1.00
 O A:HOH818 2.2 51.6 1.0
O A:HOH734 2.2 50.8 1.0
O A:TYR245 2.2 35.0 1.0
O A:HIS242 2.2 36.5 1.0
O A:HOH718 2.5 36.5 1.0
C A:HIS242 3.4 35.3 1.0
C A:TYR245 3.4 34.4 1.0
O A:HOH813 4.0 54.2 1.0
CD2 A:TYR245 4.1 31.7 1.0
CA A:HIS242 4.1 35.0 1.0
CE2 A:TYR245 4.1 30.0 1.0
CB A:HIS242 4.2 35.1 1.0
CG A:TYR245 4.2 31.7 1.0
N A:THR246 4.3 34.6 1.0
CA A:THR246 4.3 34.7 1.0
N A:TYR245 4.3 33.5 1.0
CZ A:TYR245 4.4 31.2 1.0
CA A:TYR245 4.4 33.7 1.0
N A:SER243 4.4 35.5 1.0
CD1 A:TYR245 4.4 31.9 1.0
CE1 A:TYR245 4.5 30.8 1.0
CA A:SER243 4.6 35.7 1.0
O A:HOH802 4.7 52.5 1.0
C A:SER243 4.9 35.5 1.0
CB A:TYR245 4.9 32.9 1.0
C A:THR246 5.0 35.0 1.0
O A:GLY247 5.0 33.0 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 20:55:23 2024

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