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Fluorine 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:

Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 2 binding sites of Fluorine 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 Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5f01

Go back to Fluorine Binding Sites List in 5f01
Fluorine 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 Fluorine with other atoms in the F 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:F504

b:23.5
occ:1.00
 F14 A:5T7504 0.0 23.5 1.0
C2 A:5T7504 1.4 22.4 1.0
F15 A:5T7504 2.3 26.2 1.0
C3 A:5T7504 2.4 24.2 1.0
C1 A:5T7504 2.4 20.0 1.0
C9 A:5T7504 2.8 19.0 1.0
C13 A:5T7504 3.0 21.5 1.0
CG A:TYR132 3.6 26.0 1.0
O4 A:5T7504 3.6 20.9 1.0
N6 A:5T7504 3.6 18.9 1.0
CD2 A:TYR132 3.7 27.4 1.0
CD1 A:TYR132 3.8 26.8 1.0
O A:HOH914 4.0 46.3 1.0
C7 A:5T7504 4.0 19.6 1.0
CE2 A:TYR132 4.0 28.3 1.0
C5 A:5T7504 4.0 19.7 1.0
CB A:TYR132 4.1 28.6 1.0
O A:HOH977 4.1 41.0 1.0
CE1 A:TYR132 4.1 25.3 1.0
CZ A:TYR132 4.2 24.9 1.0
C8 A:5T7504 4.3 19.3 1.0
C10 A:5T7504 4.7 21.6 1.0
O11 A:5T7504 4.8 23.2 1.0

Fluorine binding site 2 out of 2 in 5f01

Go back to Fluorine Binding Sites List in 5f01
Fluorine 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 Fluorine with other atoms in the F 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:F504

b:26.2
occ:1.00
 F15 A:5T7504 0.0 26.2 1.0
C2 A:5T7504 1.4 22.4 1.0
F14 A:5T7504 2.3 23.5 1.0
C1 A:5T7504 2.4 20.0 1.0
C3 A:5T7504 2.4 24.2 1.0
O4 A:5T7504 2.7 20.9 1.0
C13 A:5T7504 2.8 21.5 1.0
N6 A:5T7504 2.9 18.9 1.0
C5 A:5T7504 3.0 19.7 1.0
O A:HOH914 3.7 46.3 1.0
CD1 A:TYR132 3.7 26.8 1.0
C9 A:5T7504 3.7 19.0 1.0
CE1 A:TYR132 3.9 25.3 1.0
N16 A:5T7504 4.1 18.9 1.0
CG A:TYR132 4.2 26.0 1.0
O A:HOH854 4.4 44.6 1.0
CZ A:TYR132 4.5 24.9 1.0
O A:HOH820 4.7 35.1 1.0
CB A:TYR132 4.8 28.6 1.0
C7 A:5T7504 4.8 19.6 1.0
CD2 A:TYR132 4.8 27.4 1.0
CE2 A:TYR132 5.0 28.3 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: Thu Aug 1 09:17:09 2024

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