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Sodium in PDB 7g3a: Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 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-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm, PDB code: 7g3a was solved by M.Stihle, J.Benz, D.Hunziker, H.Richter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.91 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.858, 91.826, 119.462, 90, 90, 90
R / Rfree (%) 18.8 / 22.6

Other elements in 7g3a:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm also contains other interesting chemical elements:

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

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-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm (pdb code 7g3a). 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-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm, PDB code: 7g3a:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g3a

Go back to Sodium Binding Sites List in 7g3a
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 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-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:30.8
occ:1.00
 OG A:SER807 2.3 24.6 1.0
O A:HOH1415 2.4 30.5 1.0
O A:SER804 2.4 22.2 1.0
O A:HOH1205 2.5 37.3 1.0
O A:ASN801 2.6 21.4 1.0
O A:HOH1292 2.6 29.8 1.0
CB A:SER807 3.4 23.7 1.0
C A:ASN801 3.4 21.8 1.0
C A:SER804 3.5 22.2 1.0
CA A:ASP802 3.9 25.4 1.0
N A:SER807 4.1 26.6 1.0
N A:ASP802 4.1 21.6 1.0
O A:HOH1055 4.1 35.7 1.0
CA A:CYS805 4.2 26.0 1.0
CA A:SER807 4.2 27.0 1.0
O A:ASP802 4.2 23.3 1.0
C A:ASP802 4.3 22.9 1.0
N A:CYS805 4.3 24.6 1.0
C A:CYS805 4.3 28.3 1.0
CB A:ASN801 4.4 22.0 1.0
CA A:SER804 4.4 19.6 1.0
N A:SER804 4.4 19.9 1.0
O A:CYS805 4.4 29.1 1.0
CA A:ASN801 4.5 21.4 1.0
O A:HOH1206 4.6 29.8 1.0
CB A:SER804 4.7 21.0 1.0
OD1 A:ASP802 4.8 28.6 1.0
N A:ASN806 4.9 26.2 1.0
O A:HOH1148 4.9 34.4 1.0
C A:SER807 5.0 28.7 1.0

Sodium binding site 2 out of 2 in 7g3a

Go back to Sodium Binding Sites List in 7g3a
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 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-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:29.7
occ:1.00
 O A:MET675 2.3 25.6 1.0
O A:ASP672 2.3 31.0 1.0
O A:TYR669 2.3 27.1 1.0
O A:HOH1397 2.3 35.2 1.0
C A:MET675 3.4 24.5 1.0
C A:TYR669 3.4 29.0 1.0
C A:ASP672 3.5 32.1 1.0
N A:MET675 4.0 25.8 1.0
CA A:TYR669 4.2 25.1 1.0
CA A:MET675 4.3 23.8 1.0
O A:HOH1446 4.3 39.9 1.0
N A:SER676 4.3 19.1 1.0
O A:LYS670 4.3 38.7 1.0
CA A:SER676 4.4 20.4 1.0
CA A:ASP672 4.4 31.0 1.0
CA A:LYS673 4.4 34.8 1.0
N A:LYS673 4.4 31.1 1.0
C A:LYS673 4.4 30.6 1.0
N A:LYS670 4.4 29.1 1.0
N A:ASP672 4.5 33.9 1.0
CB A:TYR669 4.5 23.7 1.0
CB A:ASP672 4.6 27.6 1.0
C A:LYS670 4.6 33.6 1.0
O A:LYS673 4.6 31.1 1.0
CA A:LYS670 4.7 33.7 1.0
N A:GLN674 4.8 28.0 1.0
CB A:MET675 4.8 24.8 1.0
CB A:SER676 4.9 19.6 1.0
C A:GLN674 5.0 28.1 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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