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Sodium in PDB 7g5x: Crystal Structure of Rat Autotaxin in Complex with 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-N-(2- Methoxyethyl)Benzamide, I.E. Smiles O(CC1=Nnc(=O)N1C) C1CC(C(CC1C1CC(CCC1)C(=O)Nccoc)Cl)C with IC50=0.0869125 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-N-(2- Methoxyethyl)Benzamide, I.E. Smiles O(CC1=Nnc(=O)N1C) C1CC(C(CC1C1CC(CCC1)C(=O)Nccoc)Cl)C with IC50=0.0869125 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-N-(2- Methoxyethyl)Benzamide, I.E. Smiles O(CC1=Nnc(=O)N1C) C1CC(C(CC1C1CC(CCC1)C(=O)Nccoc)Cl)C with IC50=0.0869125 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-N-(2- Methoxyethyl)Benzamide, I.E. Smiles O(CC1=Nnc(=O)N1C) C1CC(C(CC1C1CC(CCC1)C(=O)Nccoc)Cl)C with IC50=0.0869125 Microm, PDB code: 7g5x 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) 48.71 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.866, 91.529, 119.663, 90, 90, 90
R / Rfree (%) 19.4 / 23.7

Other elements in 7g5x:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-N-(2- Methoxyethyl)Benzamide, I.E. Smiles O(CC1=Nnc(=O)N1C) C1CC(C(CC1C1CC(CCC1)C(=O)Nccoc)Cl)C with IC50=0.0869125 Microm also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 3 atoms
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-N-(2- Methoxyethyl)Benzamide, I.E. Smiles O(CC1=Nnc(=O)N1C) C1CC(C(CC1C1CC(CCC1)C(=O)Nccoc)Cl)C with IC50=0.0869125 Microm (pdb code 7g5x). 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 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-N-(2- Methoxyethyl)Benzamide, I.E. Smiles O(CC1=Nnc(=O)N1C) C1CC(C(CC1C1CC(CCC1)C(=O)Nccoc)Cl)C with IC50=0.0869125 Microm, PDB code: 7g5x:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g5x

Go back to Sodium Binding Sites List in 7g5x
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-N-(2- Methoxyethyl)Benzamide, I.E. Smiles O(CC1=Nnc(=O)N1C) C1CC(C(CC1C1CC(CCC1)C(=O)Nccoc)Cl)C with IC50=0.0869125 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 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-N-(2- Methoxyethyl)Benzamide, I.E. Smiles O(CC1=Nnc(=O)N1C) C1CC(C(CC1C1CC(CCC1)C(=O)Nccoc)Cl)C with IC50=0.0869125 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:30.6
occ:1.00
 OG A:SER807 2.3 24.3 1.0
O A:HOH1361 2.4 28.4 1.0
O A:HOH1196 2.4 30.4 1.0
O A:HOH1253 2.5 34.2 1.0
O A:SER804 2.5 23.9 1.0
O A:ASN801 2.6 23.7 1.0
C A:ASN801 3.5 24.8 1.0
CB A:SER807 3.5 24.1 1.0
C A:SER804 3.6 26.2 1.0
CA A:ASP802 4.0 26.0 1.0
N A:ASP802 4.1 23.3 1.0
N A:SER807 4.1 26.1 1.0
CA A:SER807 4.3 27.9 1.0
O A:ASP802 4.3 24.6 1.0
C A:ASP802 4.3 26.2 1.0
CA A:CYS805 4.3 31.3 1.0
O A:HOH1150 4.3 39.1 1.0
N A:CYS805 4.4 27.0 1.0
CB A:ASN801 4.4 24.8 1.0
C A:CYS805 4.4 29.9 1.0
O A:HOH1091 4.4 40.8 1.0
N A:SER804 4.5 25.0 1.0
O A:CYS805 4.5 31.0 1.0
CA A:SER804 4.5 25.0 1.0
CA A:ASN801 4.5 24.6 1.0
OD1 A:ASP802 4.8 28.6 1.0
CB A:SER804 4.9 25.6 1.0
O A:HOH1208 4.9 31.4 1.0
C A:SER807 4.9 30.7 1.0
N A:ASN806 5.0 30.8 1.0

Sodium binding site 2 out of 2 in 7g5x

Go back to Sodium Binding Sites List in 7g5x
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-N-(2- Methoxyethyl)Benzamide, I.E. Smiles O(CC1=Nnc(=O)N1C) C1CC(C(CC1C1CC(CCC1)C(=O)Nccoc)Cl)C with IC50=0.0869125 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 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-N-(2- Methoxyethyl)Benzamide, I.E. Smiles O(CC1=Nnc(=O)N1C) C1CC(C(CC1C1CC(CCC1)C(=O)Nccoc)Cl)C with IC50=0.0869125 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:17.2
occ:1.00
 O A:ASP672 2.2 29.1 1.0
O A:TYR669 2.3 29.1 1.0
O A:MET675 2.3 26.5 1.0
O A:HOH1349 2.3 40.7 1.0
O A:HOH1304 2.3 26.5 1.0
O A:HOH1355 2.4 41.5 1.0
C A:MET675 3.4 25.3 1.0
C A:ASP672 3.4 31.0 1.0
C A:TYR669 3.5 29.2 1.0
N A:MET675 4.1 28.4 1.0
CA A:TYR669 4.2 26.4 1.0
N A:SER676 4.3 21.2 1.0
CA A:LYS673 4.3 33.0 1.0
CA A:SER676 4.3 21.9 1.0
O A:LYS670 4.3 33.5 1.0
N A:LYS673 4.3 30.1 1.0
CA A:MET675 4.3 26.2 1.0
C A:LYS673 4.4 31.9 1.0
CA A:ASP672 4.4 29.7 1.0
N A:LYS670 4.5 30.8 1.0
CB A:ASP672 4.5 28.4 1.0
O A:LYS673 4.5 30.9 1.0
CB A:TYR669 4.6 24.4 1.0
N A:ASP672 4.7 32.1 1.0
C A:LYS670 4.7 31.6 1.0
CA A:LYS670 4.7 33.0 1.0
CB A:SER676 4.8 22.1 1.0
N A:GLN674 4.8 32.0 1.0
C A:GLN674 4.9 32.2 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 23:25:46 2025

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