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Sodium in PDB 5ezx: Crystal Structure of Bace-1 in Complex with {(1R,2R)-2-[(R)-2-Amino-4- (4-Difluoromethoxy-Phenyl)-4,5-Dihydro-Oxazol-4-Yl]-Cyclopropyl}-(5- Chloro-Pyridin-3-Yl)-Methanone

Enzymatic activity of Crystal Structure of Bace-1 in Complex with {(1R,2R)-2-[(R)-2-Amino-4- (4-Difluoromethoxy-Phenyl)-4,5-Dihydro-Oxazol-4-Yl]-Cyclopropyl}-(5- Chloro-Pyridin-3-Yl)-Methanone

All present enzymatic activity of Crystal Structure of Bace-1 in Complex with {(1R,2R)-2-[(R)-2-Amino-4- (4-Difluoromethoxy-Phenyl)-4,5-Dihydro-Oxazol-4-Yl]-Cyclopropyl}-(5- Chloro-Pyridin-3-Yl)-Methanone:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Bace-1 in Complex with {(1R,2R)-2-[(R)-2-Amino-4- (4-Difluoromethoxy-Phenyl)-4,5-Dihydro-Oxazol-4-Yl]-Cyclopropyl}-(5- Chloro-Pyridin-3-Yl)-Methanone, PDB code: 5ezx 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) 47.73 / 1.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.320, 102.320, 169.820, 90.00, 90.00, 120.00
R / Rfree (%) 20.8 / 23.6

Other elements in 5ezx:

The structure of Crystal Structure of Bace-1 in Complex with {(1R,2R)-2-[(R)-2-Amino-4- (4-Difluoromethoxy-Phenyl)-4,5-Dihydro-Oxazol-4-Yl]-Cyclopropyl}-(5- Chloro-Pyridin-3-Yl)-Methanone 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 {(1R,2R)-2-[(R)-2-Amino-4- (4-Difluoromethoxy-Phenyl)-4,5-Dihydro-Oxazol-4-Yl]-Cyclopropyl}-(5- Chloro-Pyridin-3-Yl)-Methanone (pdb code 5ezx). 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 {(1R,2R)-2-[(R)-2-Amino-4- (4-Difluoromethoxy-Phenyl)-4,5-Dihydro-Oxazol-4-Yl]-Cyclopropyl}-(5- Chloro-Pyridin-3-Yl)-Methanone, PDB code: 5ezx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5ezx

Go back to Sodium Binding Sites List in 5ezx
Sodium binding site 1 out of 2 in the Crystal Structure of Bace-1 in Complex with {(1R,2R)-2-[(R)-2-Amino-4- (4-Difluoromethoxy-Phenyl)-4,5-Dihydro-Oxazol-4-Yl]-Cyclopropyl}-(5- Chloro-Pyridin-3-Yl)-Methanone


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 {(1R,2R)-2-[(R)-2-Amino-4- (4-Difluoromethoxy-Phenyl)-4,5-Dihydro-Oxazol-4-Yl]-Cyclopropyl}-(5- Chloro-Pyridin-3-Yl)-Methanone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:49.6
occ:1.00
 O A:TYR245 2.3 26.4 1.0
O A:HOH710 2.4 48.1 1.0
O A:HOH697 2.4 34.7 1.0
O A:HIS242 2.5 28.2 1.0
O A:HOH922 3.3 59.5 1.0
C A:TYR245 3.4 26.3 1.0
C A:HIS242 3.6 27.9 1.0
O A:HOH808 3.6 42.2 1.0
CD2 A:TYR245 4.0 27.7 1.0
CE2 A:TYR245 4.0 27.5 1.0
CB A:HIS242 4.1 27.7 1.0
CA A:HIS242 4.2 27.2 1.0
CG A:TYR245 4.2 25.6 1.0
CZ A:TYR245 4.2 28.6 1.0
CA A:THR246 4.2 27.4 1.0
N A:THR246 4.3 27.1 1.0
CD1 A:TYR245 4.4 27.6 1.0
CE1 A:TYR245 4.4 27.2 1.0
CA A:TYR245 4.4 26.5 1.0
N A:TYR245 4.5 26.4 1.0
O A:HOH744 4.6 52.0 1.0
N A:SER243 4.6 28.3 1.0
O A:GLY247 4.8 26.4 1.0
OH A:TYR245 4.8 30.1 1.0
C A:THR246 4.9 28.0 1.0
CA A:SER243 4.9 28.6 1.0
CB A:TYR245 4.9 26.3 1.0
O A:HOH708 5.0 50.1 1.0

Sodium binding site 2 out of 2 in 5ezx

Go back to Sodium Binding Sites List in 5ezx
Sodium binding site 2 out of 2 in the Crystal Structure of Bace-1 in Complex with {(1R,2R)-2-[(R)-2-Amino-4- (4-Difluoromethoxy-Phenyl)-4,5-Dihydro-Oxazol-4-Yl]-Cyclopropyl}-(5- Chloro-Pyridin-3-Yl)-Methanone


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 {(1R,2R)-2-[(R)-2-Amino-4- (4-Difluoromethoxy-Phenyl)-4,5-Dihydro-Oxazol-4-Yl]-Cyclopropyl}-(5- Chloro-Pyridin-3-Yl)-Methanone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:39.2
occ:1.00
 O A:HOH875 2.2 50.3 1.0
O A:HOH661 2.2 53.8 1.0
O A:VAL202 2.3 33.4 1.0
O A:HOH729 2.3 33.4 1.0
O A:THR205 2.6 32.2 1.0
O A:HOH888 2.8 49.9 1.0
C A:VAL202 3.5 32.7 1.0
C A:THR205 3.8 32.1 1.0
O A:HOH927 3.9 48.3 1.0
CG1 A:VAL202 4.2 30.1 1.0
O A:LYS203 4.3 34.5 1.0
CA A:VAL202 4.3 31.4 1.0
CA A:HIS206 4.4 33.1 1.0
C A:LYS203 4.4 33.6 1.0
N A:LYS203 4.5 33.1 1.0
N A:THR205 4.5 31.7 1.0
CA A:LYS203 4.6 34.0 1.0
N A:HIS206 4.6 32.1 1.0
O A:VAL207 4.7 27.0 1.0
CA A:THR205 4.8 32.0 1.0
C A:HIS206 4.8 31.9 1.0
CB A:VAL202 4.9 31.0 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 20:55:19 2024

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