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Sodium in PDB 5f01: Crystal Structure of Bace-1 in Complex with (1SR,2SR)-2-((R)-2-Amino- 5,5-Difluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-N-(3- Chloroquinolin-8-Yl)Cyclopropanecarboxamide

Enzymatic activity of Crystal Structure of Bace-1 in Complex with (1SR,2SR)-2-((R)-2-Amino- 5,5-Difluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-N-(3- Chloroquinolin-8-Yl)Cyclopropanecarboxamide

All present enzymatic activity of Crystal Structure of Bace-1 in Complex with (1SR,2SR)-2-((R)-2-Amino- 5,5-Difluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-N-(3- Chloroquinolin-8-Yl)Cyclopropanecarboxamide:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Bace-1 in Complex with (1SR,2SR)-2-((R)-2-Amino- 5,5-Difluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-N-(3- Chloroquinolin-8-Yl)Cyclopropanecarboxamide, PDB code: 5f01 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) 47.78 / 1.52
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.413, 102.413, 170.162, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 20.6

Other elements in 5f01:

The structure of Crystal Structure of Bace-1 in Complex with (1SR,2SR)-2-((R)-2-Amino- 5,5-Difluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-N-(3- Chloroquinolin-8-Yl)Cyclopropanecarboxamide 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 (1SR,2SR)-2-((R)-2-Amino- 5,5-Difluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-N-(3- Chloroquinolin-8-Yl)Cyclopropanecarboxamide (pdb code 5f01). 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 (1SR,2SR)-2-((R)-2-Amino- 5,5-Difluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-N-(3- Chloroquinolin-8-Yl)Cyclopropanecarboxamide, PDB code: 5f01:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5f01

Go back to Sodium Binding Sites List in 5f01
Sodium binding site 1 out of 2 in the Crystal Structure of Bace-1 in Complex with (1SR,2SR)-2-((R)-2-Amino- 5,5-Difluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-N-(3- Chloroquinolin-8-Yl)Cyclopropanecarboxamide


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 (1SR,2SR)-2-((R)-2-Amino- 5,5-Difluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-N-(3- Chloroquinolin-8-Yl)Cyclopropanecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:38.0
occ:1.00
 O A:TYR245 2.3 21.1 1.0
O A:HOH767 2.4 29.8 1.0
O A:HOH937 2.4 53.1 1.0
O A:HOH906 2.4 41.9 1.0
O A:HIS242 2.5 24.4 1.0
C A:TYR245 3.5 19.6 1.0
C A:HIS242 3.7 22.3 1.0
O A:HOH844 3.8 37.6 1.0
CD2 A:TYR245 4.0 21.0 1.0
CE2 A:TYR245 4.1 20.1 1.0
CA A:THR246 4.1 21.4 1.0
N A:THR246 4.2 19.4 1.0
O A:HOH766 4.2 48.1 1.0
CG A:TYR245 4.3 20.2 1.0
CB A:HIS242 4.4 26.4 1.0
CZ A:TYR245 4.4 21.8 1.0
CA A:HIS242 4.4 23.2 1.0
N A:TYR245 4.4 19.7 1.0
CA A:TYR245 4.5 19.1 1.0
CD1 A:TYR245 4.5 19.9 1.0
CE1 A:TYR245 4.6 20.8 1.0
N A:SER243 4.7 23.9 1.0
O A:HOH798 4.7 39.5 1.0
C A:THR246 4.8 23.2 1.0
O A:GLY247 4.9 22.1 1.0
CA A:SER243 4.9 26.3 1.0
CB A:TYR245 5.0 19.2 1.0

Sodium binding site 2 out of 2 in 5f01

Go back to Sodium Binding Sites List in 5f01
Sodium binding site 2 out of 2 in the Crystal Structure of Bace-1 in Complex with (1SR,2SR)-2-((R)-2-Amino- 5,5-Difluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-N-(3- Chloroquinolin-8-Yl)Cyclopropanecarboxamide


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 (1SR,2SR)-2-((R)-2-Amino- 5,5-Difluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-N-(3- Chloroquinolin-8-Yl)Cyclopropanecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:33.9
occ:1.00
 O A:VAL202 2.3 26.4 1.0
O A:HOH938 2.4 44.0 1.0
O A:HOH675 2.4 32.8 1.0
O A:THR205 2.4 31.6 1.0
O A:HOH799 2.4 43.9 1.0
O A:HOH869 2.5 47.0 1.0
C A:VAL202 3.5 26.0 1.0
C A:THR205 3.6 27.5 1.0
CA A:HIS206 4.2 33.7 1.0
CG1 A:VAL202 4.2 25.7 1.0
CA A:VAL202 4.3 24.0 1.0
N A:HIS206 4.4 31.7 1.0
O A:LYS203 4.4 29.5 1.0
N A:THR205 4.4 27.5 1.0
O A:HOH941 4.5 54.9 1.0
C A:LYS203 4.5 27.3 1.0
N A:LYS203 4.5 23.8 1.0
O A:VAL207 4.6 22.5 1.0
CA A:LYS203 4.7 27.7 1.0
CA A:THR205 4.7 27.2 1.0
C A:HIS206 4.7 32.3 1.0
ND1 A:HIS206 4.9 50.0 1.0
N A:VAL207 4.9 27.3 1.0
CB A:VAL202 4.9 23.6 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 20:57:17 2024

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