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Sodium in PDB 7g3g: Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm, PDB code: 7g3g was solved by M.Stihle, J.Benz, D.Hunziker, H.Ratni, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.31 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.728, 91.178, 118.716, 90, 90, 90
R / Rfree (%) 16.9 / 20.4

Other elements in 7g3g:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm (pdb code 7g3g). 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 Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm, PDB code: 7g3g:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g3g

Go back to Sodium Binding Sites List in 7g3g
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm


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 Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:33.1
occ:1.00
 OG A:SER807 2.3 29.6 1.0
O A:SER804 2.3 27.8 1.0
O A:HOH1243 2.4 33.3 1.0
O A:HOH1029 2.5 32.7 1.0
O A:HOH1370 2.5 42.0 1.0
O A:ASN801 2.5 25.6 1.0
C A:SER804 3.4 27.6 1.0
C A:ASN801 3.4 25.5 1.0
CB A:SER807 3.4 30.8 1.0
CA A:ASP802 3.8 29.9 1.0
N A:ASP802 4.0 26.0 1.0
N A:SER807 4.1 31.5 1.0
O A:HOH1403 4.1 54.0 1.0
O A:HOH1034 4.1 47.7 1.0
N A:CYS805 4.2 28.5 1.0
CA A:CYS805 4.2 34.4 1.0
C A:ASP802 4.2 29.1 1.0
O A:ASP802 4.2 26.5 1.0
CA A:SER807 4.3 33.1 1.0
C A:CYS805 4.3 33.2 1.0
N A:SER804 4.4 26.4 1.0
CA A:SER804 4.4 25.7 1.0
CB A:ASN801 4.4 26.1 1.0
O A:CYS805 4.4 35.7 1.0
CA A:ASN801 4.5 27.7 1.0
O A:HOH1142 4.5 40.1 1.0
OD1 A:ASP802 4.5 34.2 1.0
CB A:SER804 4.8 28.4 1.0
N A:ASN806 4.9 34.8 1.0
O A:HOH1296 4.9 43.1 1.0
N A:GLU803 5.0 27.8 1.0

Sodium binding site 2 out of 2 in 7g3g

Go back to Sodium Binding Sites List in 7g3g
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm


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 Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na910

b:19.2
occ:1.00
 O A:ASP672 2.1 30.4 1.0
O A:ACT905 2.2 34.7 1.0
O A:HOH1352 2.2 35.3 1.0
O A:TYR669 2.2 31.5 1.0
O A:MET675 2.3 31.3 1.0
O A:HOH1254 2.3 35.4 1.0
C A:ACT905 3.4 43.6 1.0
C A:ASP672 3.4 31.3 1.0
C A:MET675 3.4 30.1 1.0
C A:TYR669 3.4 33.5 1.0
N A:MET675 4.0 32.6 1.0
CH3 A:ACT905 4.1 40.0 1.0
CA A:TYR669 4.2 28.5 1.0
N A:LYS673 4.3 30.3 1.0
CA A:LYS673 4.3 35.5 1.0
N A:SER676 4.3 27.2 1.0
O A:LYS670 4.3 37.7 1.0
OXT A:ACT905 4.3 42.1 1.0
CA A:MET675 4.3 29.9 1.0
CA A:ASP672 4.3 31.9 1.0
C A:LYS673 4.4 34.8 1.0
CA A:SER676 4.4 24.4 1.0
N A:LYS670 4.4 37.2 1.0
N A:ASP672 4.5 34.6 1.0
CB A:ASP672 4.6 33.4 1.0
CA A:LYS670 4.6 38.2 1.0
C A:LYS670 4.6 34.2 1.0
O A:LYS673 4.6 34.4 1.0
CB A:TYR669 4.7 27.6 1.0
N A:GLN674 4.8 34.4 1.0
C A:GLN674 4.9 36.4 1.0
CB A:SER676 4.9 25.9 1.0

Reference:

D.Hunziker, S.C.Joachim, C.Ullmer, M.G.Rudolph. Crystal Structure of A Rat Autotaxin Complex To Be Published.
Page generated: Sat Feb 8 23:12:39 2025

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