Atomistry » Fluorine » PDB 4j0v-4jps » 4j0z
Atomistry »
  Fluorine »
    PDB 4j0v-4jps »
      4j0z »

Fluorine in PDB 4j0z: Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,5R)-2-Amino-5-Fluoro-4-Fluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide

Enzymatic activity of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,5R)-2-Amino-5-Fluoro-4-Fluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide

All present enzymatic activity of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,5R)-2-Amino-5-Fluoro-4-Fluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,5R)-2-Amino-5-Fluoro-4-Fluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j0z was solved by A.Kuglstatter, M.Stihle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.95 / 2.13
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.764, 102.764, 170.754, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 22.3

Other elements in 4j0z:

The structure of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,5R)-2-Amino-5-Fluoro-4-Fluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,5R)-2-Amino-5-Fluoro-4-Fluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide (pdb code 4j0z). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,5R)-2-Amino-5-Fluoro-4-Fluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j0z:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4j0z

Go back to Fluorine Binding Sites List in 4j0z
Fluorine binding site 1 out of 3 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,5R)-2-Amino-5-Fluoro-4-Fluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide


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 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,5R)-2-Amino-5-Fluoro-4-Fluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:32.3
occ:1.00
F7 A:1H5504 0.0 32.3 1.0
C4 A:1H5504 1.4 30.2 1.0
C5 A:1H5504 2.4 28.2 1.0
C3 A:1H5504 2.4 28.8 1.0
C9 A:1H5504 2.6 31.4 1.0
C8 A:1H5504 2.8 29.6 1.0
C10 A:1H5504 3.1 30.5 1.0
CE2 A:TYR132 3.1 38.8 1.0
CE1 A:PHE169 3.3 21.3 1.0
CD2 A:TYR132 3.4 36.0 1.0
CD1 A:PHE169 3.5 21.6 1.0
CZ A:TYR132 3.6 36.8 1.0
C6 A:1H5504 3.6 27.8 1.0
C2 A:1H5504 3.6 30.1 1.0
F28 A:1H5504 3.8 34.9 1.0
F15 A:1H5504 4.0 34.1 1.0
CG A:TYR132 4.1 38.7 1.0
C1 A:1H5504 4.1 28.8 1.0
OH A:TYR132 4.1 39.3 1.0
N14 A:1H5504 4.2 27.6 1.0
C11 A:1H5504 4.2 30.0 1.0
CD1 A:ILE179 4.3 25.4 0.7
CE1 A:TYR132 4.3 33.7 1.0
CD1 A:TYR132 4.4 37.5 1.0
CZ A:PHE169 4.5 21.3 1.0
CG A:PHE169 4.9 21.7 1.0
CB A:TYR132 5.0 38.2 1.0

Fluorine binding site 2 out of 3 in 4j0z

Go back to Fluorine Binding Sites List in 4j0z
Fluorine binding site 2 out of 3 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,5R)-2-Amino-5-Fluoro-4-Fluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide


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 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,5R)-2-Amino-5-Fluoro-4-Fluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:34.1
occ:1.00
F15 A:1H5504 0.0 34.1 1.0
C10 A:1H5504 1.4 30.5 1.0
C11 A:1H5504 2.3 30.0 1.0
C8 A:1H5504 2.4 29.6 1.0
F28 A:1H5504 2.7 34.9 1.0
O12 A:1H5504 2.7 30.2 1.0
N14 A:1H5504 2.8 27.6 1.0
C13 A:1H5504 2.9 28.2 1.0
C9 A:1H5504 3.0 31.4 1.0
CD1 A:TYR132 3.4 37.5 1.0
C5 A:1H5504 3.7 28.2 1.0
CE1 A:TYR132 3.7 33.7 1.0
N16 A:1H5504 4.0 27.7 1.0
CG A:TYR132 4.0 38.7 1.0
F7 A:1H5504 4.0 32.3 1.0
O A:HOH1137 4.2 41.8 1.0
C4 A:1H5504 4.3 30.2 1.0
CZ A:TYR132 4.4 36.8 1.0
O A:HOH1224 4.4 45.4 1.0
CB A:TYR132 4.5 38.2 1.0
C6 A:1H5504 4.6 27.8 1.0
CD2 A:TYR132 4.7 36.0 1.0
CE2 A:TYR132 4.8 38.8 1.0
OD2 A:ASP93 4.9 30.4 1.0

Fluorine binding site 3 out of 3 in 4j0z

Go back to Fluorine Binding Sites List in 4j0z
Fluorine binding site 3 out of 3 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,5R)-2-Amino-5-Fluoro-4-Fluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,5R)-2-Amino-5-Fluoro-4-Fluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:34.9
occ:1.00
F28 A:1H5504 0.0 34.9 1.0
C9 A:1H5504 1.4 31.4 1.0
C8 A:1H5504 2.3 29.6 1.0
N14 A:1H5504 2.6 27.6 1.0
F15 A:1H5504 2.7 34.1 1.0
C10 A:1H5504 3.0 30.5 1.0
CE1 A:TYR132 3.3 33.7 1.0
OD2 A:ASP93 3.3 30.4 1.0
CB A:SER96 3.4 23.5 1.0
CZ A:TYR132 3.5 36.8 1.0
OH A:TYR132 3.5 39.3 1.0
C5 A:1H5504 3.6 28.2 1.0
OG A:SER96 3.6 21.2 1.0
C13 A:1H5504 3.6 28.2 1.0
O A:HOH1120 3.7 43.3 1.0
F7 A:1H5504 3.8 32.3 1.0
CD1 A:TYR132 4.0 37.5 1.0
C4 A:1H5504 4.1 30.2 1.0
O A:HOH1221 4.1 58.5 1.0
C11 A:1H5504 4.3 30.0 1.0
O12 A:1H5504 4.4 30.2 1.0
CE2 A:TYR132 4.4 38.8 1.0
O A:HOH1014 4.4 22.3 1.0
O A:HOH1137 4.4 41.8 1.0
N16 A:1H5504 4.4 27.7 1.0
CG A:ASP93 4.5 27.0 1.0
C6 A:1H5504 4.6 27.8 1.0
CA A:SER96 4.8 22.9 1.0
CG A:TYR132 4.9 38.7 1.0
CD1 A:ILE179 4.9 25.4 0.7
CD2 A:TYR132 5.0 36.0 1.0

Reference:

H.Hilpert, W.Guba, T.J.Woltering, W.Wostl, E.Pinard, H.Mauser, A.V.Mayweg, M.Rogers-Evans, R.Humm, D.Krummenacher, T.Muser, C.Schnider, H.Jacobsen, L.Ozmen, A.Bergadano, D.W.Banner, R.Hochstrasser, A.Kuglstatter, P.David-Pierson, H.Fischer, A.Polara, R.Narquizian. Beta-Secretase (BACE1) Inhibitors with High in Vivo Efficacy Suitable For Clinical Evaluation in Alzheimer S Disease J.Med.Chem. V. 56 3980 2013.
ISSN: ISSN 0022-2623
PubMed: 23590342
DOI: 10.1021/JM400225M
Page generated: Sun Dec 13 12:05:05 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy