Atomistry » Sodium » PDB 4j0p-4jer » 4j1f
Atomistry »
  Sodium »
    PDB 4j0p-4jer »
      4j1f »

Sodium in PDB 4j1f: Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6S)-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,6S)-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,6S)-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,6S)-2-Amino-4-Methyl-6-Trifluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j1f 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) 47.97 / 2.25
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 103.495, 103.495, 170.358, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 24.9

Other elements in 4j1f:

The structure of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6S)-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:

Fluorine (F) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6S)-2-Amino-4-Methyl-6-Trifluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide (pdb code 4j1f). 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 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6S)-2-Amino-4-Methyl-6-Trifluoromethyl-5,6- Dihydro-4H-[1,3]Oxazin-4-Yl)-4-Fluoro-Phenyl]-Amide, PDB code: 4j1f:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4j1f

Go back to Sodium Binding Sites List in 4j1f
Sodium binding site 1 out of 2 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6S)-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 Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6S)-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:Na501

b:61.5
occ:1.00
 O A:HIS242 2.6 42.1 1.0
O A:HOH1062 2.9 57.0 1.0
O A:TYR245 3.0 38.2 1.0
C A:HIS242 3.5 41.5 1.0
CB A:HIS242 3.9 47.3 1.0
CE2 A:TYR245 4.0 32.9 1.0
CA A:HIS242 4.0 41.5 1.0
C A:TYR245 4.0 36.4 1.0
CZ A:TYR245 4.1 33.0 1.0
CD2 A:TYR245 4.2 33.6 1.0
CE1 A:TYR245 4.4 30.9 1.0
CG A:TYR245 4.5 31.8 1.0
OH A:TYR245 4.6 36.5 1.0
CD1 A:TYR245 4.6 30.8 1.0
N A:SER243 4.6 42.6 1.0
CA A:THR246 4.7 38.3 1.0
N A:THR246 4.8 34.4 1.0
N A:TYR245 4.9 35.5 1.0
O A:GLY247 4.9 36.7 1.0
CG A:HIS242 4.9 52.8 1.0
CA A:TYR245 5.0 33.9 1.0

Sodium binding site 2 out of 2 in 4j1f

Go back to Sodium Binding Sites List in 4j1f
Sodium binding site 2 out of 2 in the Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6S)-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 Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Bace-1 in Complex with 5-Cyano-Pyridine-2- Carboxylic Acid [3-((4S,6S)-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:Na502

b:59.1
occ:1.00
 O A:VAL202 2.6 43.2 1.0
O A:THR205 2.7 51.0 1.0
C A:VAL202 3.7 39.7 1.0
C A:THR205 3.9 50.0 1.0
CG1 A:VAL202 4.1 35.5 1.0
CA A:VAL202 4.4 35.6 1.0
CA A:HIS206 4.4 54.9 1.0
O A:VAL207 4.5 40.5 1.0
O A:LYS203 4.6 47.4 1.0
N A:HIS206 4.7 51.4 1.0
N A:LYS203 4.7 39.2 1.0
C A:LYS203 4.7 45.0 1.0
N A:THR205 4.8 47.0 1.0
C A:HIS206 4.8 48.0 1.0
CA A:LYS203 4.9 44.2 1.0
CB A:VAL202 4.9 35.9 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 Oct 7 16:10:50 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy