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Fluorine in PDB 4j1h: Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6R)-2-Amino-4-Methyl-6-Trifluoromethyl-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,6R)-2-Amino-4-Methyl-6-Trifluoromethyl-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,6R)-2-Amino-4-Methyl-6-Trifluoromethyl-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,6R)-2-Amino-4-Methyl-6-Trifluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j1h 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) 47.56 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.685, 102.685, 168.873, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 23.6

Other elements in 4j1h:

The structure of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6R)-2-Amino-4-Methyl-6-Trifluoromethyl-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,6R)-2-Amino-4-Methyl-6-Trifluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide (pdb code 4j1h). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6R)-2-Amino-4-Methyl-6-Trifluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j1h:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4j1h

Go back to Fluorine Binding Sites List in 4j1h
Fluorine binding site 1 out of 4 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6R)-2-Amino-4-Methyl-6-Trifluoromethyl-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,6R)-2-Amino-4-Methyl-6-Trifluoromethyl-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:41.2
occ:1.00
 F13 A:1HJ504 0.0 41.2 1.0
C12 A:1HJ504 1.3 38.6 1.0
C11 A:1HJ504 2.3 42.2 1.0
C7 A:1HJ504 2.4 32.7 1.0
C15 A:1HJ504 2.8 29.5 1.0
C6 A:1HJ504 2.9 34.0 1.0
C2 A:1HJ504 3.1 34.5 1.0
CE1 A:PHE169 3.3 32.3 1.0
CE2 A:TYR132 3.3 35.9 0.5
CD1 A:PHE169 3.5 30.3 1.0
C10 A:1HJ504 3.6 38.6 1.0
C8 A:1HJ504 3.6 30.6 1.0
CD2 A:TYR132 3.6 36.5 0.5
CZ A:TYR132 4.0 36.3 0.5
C9 A:1HJ504 4.0 34.3 1.0
CD1 A:ILE179 4.1 33.5 0.7
N5 A:1HJ504 4.3 31.2 1.0
O A:HOH1039 4.4 54.6 1.0
CG A:TYR132 4.4 36.8 0.5
OH A:TYR132 4.5 37.7 0.5
CZ A:PHE169 4.5 31.5 1.0
C1 A:1HJ504 4.6 39.3 1.0
CE1 A:TYR132 4.7 35.2 0.5
CG A:PHE169 4.9 31.8 1.0
CD1 A:TYR132 4.9 35.5 0.5
O A:HOH1123 5.0 46.5 1.0

Fluorine binding site 2 out of 4 in 4j1h

Go back to Fluorine Binding Sites List in 4j1h
Fluorine binding site 2 out of 4 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6R)-2-Amino-4-Methyl-6-Trifluoromethyl-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,6R)-2-Amino-4-Methyl-6-Trifluoromethyl-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:49.4
occ:1.00
 F28 A:1HJ504 0.0 49.4 1.0
C27 A:1HJ504 1.4 46.3 1.0
F29 A:1HJ504 2.2 42.0 1.0
F30 A:1HJ504 2.3 47.7 1.0
C1 A:1HJ504 2.4 39.3 1.0
C2 A:1HJ504 2.9 34.5 1.0
CD1 A:TYR132 3.1 35.5 0.5
O A:HOH1115 3.1 59.4 1.0
O3 A:1HJ504 3.6 31.7 1.0
CG A:TYR132 3.6 36.8 0.5
CE1 A:TYR132 3.8 35.2 0.5
CB A:TYR132 3.8 40.3 0.5
C6 A:1HJ504 4.3 34.0 1.0
CD2 A:TYR132 4.6 36.5 0.5
CA A:TYR132 4.6 48.6 0.5
C4 A:1HJ504 4.7 32.4 1.0
CZ A:TYR132 4.7 36.3 0.5
C15 A:1HJ504 4.9 29.5 1.0
O A:HOH1118 4.9 47.7 1.0
N5 A:1HJ504 5.0 31.2 1.0
N A:THR133 5.0 72.4 1.0

Fluorine binding site 3 out of 4 in 4j1h

Go back to Fluorine Binding Sites List in 4j1h
Fluorine binding site 3 out of 4 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6R)-2-Amino-4-Methyl-6-Trifluoromethyl-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,6R)-2-Amino-4-Methyl-6-Trifluoromethyl-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:42.0
occ:1.00
 F29 A:1HJ504 0.0 42.0 1.0
C27 A:1HJ504 1.4 46.3 1.0
F28 A:1HJ504 2.2 49.4 1.0
C1 A:1HJ504 2.3 39.3 1.0
F30 A:1HJ504 2.4 47.7 1.0
O3 A:1HJ504 2.8 31.7 1.0
C2 A:1HJ504 3.7 34.5 1.0
C4 A:1HJ504 4.0 32.4 1.0
O A:HOH1115 4.1 59.4 1.0
N14 A:1HJ504 4.7 29.1 1.0
O A:HOH1118 4.7 47.7 1.0
N5 A:1HJ504 4.8 31.2 1.0
C6 A:1HJ504 4.9 34.0 1.0

Fluorine binding site 4 out of 4 in 4j1h

Go back to Fluorine Binding Sites List in 4j1h
Fluorine binding site 4 out of 4 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6R)-2-Amino-4-Methyl-6-Trifluoromethyl-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 4 of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6R)-2-Amino-4-Methyl-6-Trifluoromethyl-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:47.7
occ:1.00
 F30 A:1HJ504 0.0 47.7 1.0
C27 A:1HJ504 1.4 46.3 1.0
F28 A:1HJ504 2.3 49.4 1.0
F29 A:1HJ504 2.4 42.0 1.0
C1 A:1HJ504 2.5 39.3 1.0
O3 A:1HJ504 2.8 31.7 1.0
C2 A:1HJ504 2.9 34.5 1.0
C4 A:1HJ504 4.0 32.4 1.0
C6 A:1HJ504 4.2 34.0 1.0
N5 A:1HJ504 4.5 31.2 1.0
C7 A:1HJ504 4.6 32.7 1.0
O A:HOH1115 4.9 59.4 1.0
C8 A:1HJ504 4.9 30.6 1.0
N14 A:1HJ504 5.0 29.1 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: Mon Jul 14 22:30:47 2025

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