Atomistry » Sodium » PDB 5en3-5f00 » 5ezz
Atomistry »
  Sodium »
    PDB 5en3-5f00 »
      5ezz »

Sodium in PDB 5ezz: Crystal Structure of Bace-1 in Complex with (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine

Enzymatic activity of Crystal Structure of Bace-1 in Complex with (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine

All present enzymatic activity of Crystal Structure of Bace-1 in Complex with (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Bace-1 in Complex with (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine, PDB code: 5ezz 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) 47.84 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.670, 102.670, 170.120, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / 24

Other elements in 5ezz:

The structure of Crystal Structure of Bace-1 in Complex with (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Bace-1 in Complex with (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine (pdb code 5ezz). 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 (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine, PDB code: 5ezz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5ezz

Go back to Sodium Binding Sites List in 5ezz
Sodium binding site 1 out of 2 in the Crystal Structure of Bace-1 in Complex with (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine


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 (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:41.6
occ:1.00
 O A:VAL202 2.2 40.9 1.0
O A:THR205 2.3 40.9 1.0
O A:HOH698 2.4 45.8 1.0
O A:HOH823 3.0 56.1 1.0
C A:VAL202 3.4 40.6 1.0
C A:THR205 3.5 40.7 1.0
O A:LYS203 4.2 42.0 1.0
N A:THR205 4.3 40.1 1.0
O A:HOH851 4.3 46.9 1.0
C A:LYS203 4.3 41.0 1.0
CA A:VAL202 4.3 40.0 1.0
CG1 A:VAL202 4.3 40.7 1.0
N A:LYS203 4.3 41.0 1.0
CA A:HIS206 4.4 41.9 1.0
N A:HIS206 4.4 40.8 1.0
CA A:LYS203 4.4 41.4 1.0
CA A:THR205 4.5 40.7 1.0
O A:VAL207 4.7 34.6 1.0
N A:GLN204 4.8 39.9 1.0
C A:HIS206 4.9 40.8 1.0
CB A:VAL202 5.0 39.9 1.0

Sodium binding site 2 out of 2 in 5ezz

Go back to Sodium Binding Sites List in 5ezz
Sodium binding site 2 out of 2 in the Crystal Structure of Bace-1 in Complex with (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine


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 (4S)-4-[3-(5-Chloro-3- Pyridyl)Phenyl]-4-[4-(Difluoromethoxy)-3-Methyl-Phenyl]-5H-Oxazol-2- Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:37.9
occ:1.00
 O A:HOH818 2.2 51.6 1.0
O A:HOH734 2.2 50.8 1.0
O A:TYR245 2.2 35.0 1.0
O A:HIS242 2.2 36.5 1.0
O A:HOH718 2.5 36.5 1.0
C A:HIS242 3.4 35.3 1.0
C A:TYR245 3.4 34.4 1.0
O A:HOH813 4.0 54.2 1.0
CD2 A:TYR245 4.1 31.7 1.0
CA A:HIS242 4.1 35.0 1.0
CE2 A:TYR245 4.1 30.0 1.0
CB A:HIS242 4.2 35.1 1.0
CG A:TYR245 4.2 31.7 1.0
N A:THR246 4.3 34.6 1.0
CA A:THR246 4.3 34.7 1.0
N A:TYR245 4.3 33.5 1.0
CZ A:TYR245 4.4 31.2 1.0
CA A:TYR245 4.4 33.7 1.0
N A:SER243 4.4 35.5 1.0
CD1 A:TYR245 4.4 31.9 1.0
CE1 A:TYR245 4.5 30.8 1.0
CA A:SER243 4.6 35.7 1.0
O A:HOH802 4.7 52.5 1.0
C A:SER243 4.9 35.5 1.0
CB A:TYR245 4.9 32.9 1.0
C A:THR246 5.0 35.0 1.0
O A:GLY247 5.0 33.0 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: Mon Oct 7 20:55:23 2024

Last articles

Fe in 4UH0
Fe in 4UGZ
Fe in 4UGY
Fe in 4UGX
Fe in 4UGV
Fe in 4UGW
Fe in 4UGU
Fe in 4UGT
Fe in 4UGS
Fe in 4UGR
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy