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Fluorine 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:

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

Fluorine binding site 1 out of 2 in 5ezx

Go back to Fluorine Binding Sites List in 5ezx
Fluorine 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 Fluorine with other atoms in the F 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:F501

b:52.9
occ:1.00
 F23 A:5T5501 0.0 52.9 1.0
C12 A:5T5501 1.4 52.8 1.0
F24 A:5T5501 2.3 55.2 1.0
O16 A:5T5501 2.3 50.7 1.0
O A:HOH758 3.2 38.8 1.0
C21 A:5T5501 3.3 46.5 1.0
C25 A:5T5501 3.5 44.7 1.0
NE A:ARG189 3.6 42.6 1.0
CZ A:ARG189 3.6 45.4 1.0
NH2 A:ARG189 3.7 46.5 1.0
CG A:ARG189 3.7 34.6 1.0
CG1 A:VAL130 3.7 42.6 1.0
O A:HOH768 4.1 45.1 1.0
CD A:ARG189 4.3 37.4 1.0
NH1 A:ARG189 4.3 45.2 1.0
OD1 A:ASN98 4.5 23.9 1.0
CB A:SER96 4.5 19.1 1.0
C26 A:5T5501 4.6 43.2 1.0
O A:ILE187 4.6 26.1 1.0
C18 A:5T5501 4.8 40.6 1.0
O A:HOH654 4.9 18.2 1.0
CB A:ARG189 5.0 32.0 1.0

Fluorine binding site 2 out of 2 in 5ezx

Go back to Fluorine Binding Sites List in 5ezx
Fluorine 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 Fluorine with other atoms in the F 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:F501

b:55.2
occ:1.00
 F24 A:5T5501 0.0 55.2 1.0
C12 A:5T5501 1.4 52.8 1.0
F23 A:5T5501 2.3 52.9 1.0
O16 A:5T5501 2.3 50.7 1.0
C21 A:5T5501 2.8 46.5 1.0
C25 A:5T5501 2.8 44.7 1.0
NH2 A:ARG189 3.2 46.5 1.0
O A:HOH768 3.6 45.1 1.0
CZ A:ARG189 3.7 45.4 1.0
C26 A:5T5501 3.9 43.2 1.0
C18 A:5T5501 4.0 40.6 1.0
NH1 A:ARG189 4.3 45.2 1.0
CG1 A:VAL130 4.3 42.6 1.0
CD2 A:TYR132 4.3 55.8 1.0
NE A:ARG189 4.4 42.6 1.0
CB A:TYR132 4.5 52.7 1.0
CG A:TYR132 4.7 55.1 1.0
C19 A:5T5501 4.8 41.0 1.0
C11 A:5T5501 4.9 36.7 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 09:16:31 2024

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