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Sodium in PDB 7g62: Crystal Structure of Rat Autotaxin in Complex with 3-[[4-Chloro-2-(2- Methoxypyridin-3-Yl)-5-Methylphenoxy]Methyl]-4-Methyl-1H-1,2,4- Triazol-5-One, I.E. Smiles C(C1=Nnc(=O)N1C)OC1CC(C(CC1C1C(NCCC1)Oc) Cl)C with IC50=0.253896 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[[4-Chloro-2-(2- Methoxypyridin-3-Yl)-5-Methylphenoxy]Methyl]-4-Methyl-1H-1,2,4- Triazol-5-One, I.E. Smiles C(C1=Nnc(=O)N1C)OC1CC(C(CC1C1C(NCCC1)Oc) Cl)C with IC50=0.253896 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[[4-Chloro-2-(2- Methoxypyridin-3-Yl)-5-Methylphenoxy]Methyl]-4-Methyl-1H-1,2,4- Triazol-5-One, I.E. Smiles C(C1=Nnc(=O)N1C)OC1CC(C(CC1C1C(NCCC1)Oc) Cl)C with IC50=0.253896 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[[4-Chloro-2-(2- Methoxypyridin-3-Yl)-5-Methylphenoxy]Methyl]-4-Methyl-1H-1,2,4- Triazol-5-One, I.E. Smiles C(C1=Nnc(=O)N1C)OC1CC(C(CC1C1C(NCCC1)Oc) Cl)C with IC50=0.253896 Microm, PDB code: 7g62 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) 48.69 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.914, 91.734, 119.58, 90, 90, 90
R / Rfree (%) 19.3 / 23.1

Other elements in 7g62:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[[4-Chloro-2-(2- Methoxypyridin-3-Yl)-5-Methylphenoxy]Methyl]-4-Methyl-1H-1,2,4- Triazol-5-One, I.E. Smiles C(C1=Nnc(=O)N1C)OC1CC(C(CC1C1C(NCCC1)Oc) Cl)C with IC50=0.253896 Microm also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 2 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-[[4-Chloro-2-(2- Methoxypyridin-3-Yl)-5-Methylphenoxy]Methyl]-4-Methyl-1H-1,2,4- Triazol-5-One, I.E. Smiles C(C1=Nnc(=O)N1C)OC1CC(C(CC1C1C(NCCC1)Oc) Cl)C with IC50=0.253896 Microm (pdb code 7g62). 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-[[4-Chloro-2-(2- Methoxypyridin-3-Yl)-5-Methylphenoxy]Methyl]-4-Methyl-1H-1,2,4- Triazol-5-One, I.E. Smiles C(C1=Nnc(=O)N1C)OC1CC(C(CC1C1C(NCCC1)Oc) Cl)C with IC50=0.253896 Microm, PDB code: 7g62:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g62

Go back to Sodium Binding Sites List in 7g62
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-[[4-Chloro-2-(2- Methoxypyridin-3-Yl)-5-Methylphenoxy]Methyl]-4-Methyl-1H-1,2,4- Triazol-5-One, I.E. Smiles C(C1=Nnc(=O)N1C)OC1CC(C(CC1C1C(NCCC1)Oc) Cl)C with IC50=0.253896 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-[[4-Chloro-2-(2- Methoxypyridin-3-Yl)-5-Methylphenoxy]Methyl]-4-Methyl-1H-1,2,4- Triazol-5-One, I.E. Smiles C(C1=Nnc(=O)N1C)OC1CC(C(CC1C1C(NCCC1)Oc) Cl)C with IC50=0.253896 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:39.0
occ:1.00
 O A:HOH1177 2.3 34.6 1.0
OG A:SER807 2.3 30.2 1.0
O A:HOH1363 2.3 34.8 1.0
O A:HOH1256 2.5 35.5 1.0
O A:SER804 2.5 32.8 1.0
O A:ASN801 2.6 28.1 1.0
C A:ASN801 3.4 29.7 1.0
C A:SER804 3.5 31.9 1.0
CB A:SER807 3.5 30.0 1.0
CA A:ASP802 3.8 33.8 1.0
N A:ASP802 4.0 27.9 1.0
N A:SER807 4.1 33.2 1.0
O A:ASP802 4.2 30.9 1.0
C A:ASP802 4.2 33.7 1.0
CA A:CYS805 4.2 37.7 1.0
N A:CYS805 4.3 34.2 1.0
CA A:SER807 4.3 34.1 1.0
N A:SER804 4.4 29.6 1.0
CA A:SER804 4.4 28.6 1.0
C A:CYS805 4.4 36.7 1.0
CB A:ASN801 4.4 29.7 1.0
O A:HOH1240 4.4 41.4 1.0
CA A:ASN801 4.5 29.9 1.0
O A:CYS805 4.6 40.4 1.0
OD1 A:ASP802 4.7 40.3 1.0
O A:HOH1097 4.7 45.2 1.0
CB A:SER804 4.8 32.1 1.0
O A:HOH1219 4.8 39.9 1.0
N A:ASN806 4.9 34.7 1.0

Sodium binding site 2 out of 2 in 7g62

Go back to Sodium Binding Sites List in 7g62
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-[[4-Chloro-2-(2- Methoxypyridin-3-Yl)-5-Methylphenoxy]Methyl]-4-Methyl-1H-1,2,4- Triazol-5-One, I.E. Smiles C(C1=Nnc(=O)N1C)OC1CC(C(CC1C1C(NCCC1)Oc) Cl)C with IC50=0.253896 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-[[4-Chloro-2-(2- Methoxypyridin-3-Yl)-5-Methylphenoxy]Methyl]-4-Methyl-1H-1,2,4- Triazol-5-One, I.E. Smiles C(C1=Nnc(=O)N1C)OC1CC(C(CC1C1C(NCCC1)Oc) Cl)C with IC50=0.253896 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:24.0
occ:1.00
 O A:HOH1354 2.0 43.9 1.0
O A:ASP672 2.2 37.4 1.0
O A:TYR669 2.2 33.9 1.0
O A:MET675 2.3 29.2 1.0
O A:HOH1347 2.3 31.8 1.0
O A:HOH1383 2.8 48.6 1.0
C A:ASP672 3.4 37.5 1.0
C A:TYR669 3.4 33.1 1.0
C A:MET675 3.5 31.7 1.0
N A:MET675 4.1 34.3 1.0
CA A:TYR669 4.2 31.1 1.0
N A:LYS673 4.3 35.5 1.0
CA A:ASP672 4.3 34.2 1.0
CA A:LYS673 4.3 40.3 1.0
O A:LYS670 4.3 37.8 1.0
N A:SER676 4.3 28.6 1.0
CA A:MET675 4.4 31.0 1.0
N A:LYS670 4.4 36.2 1.0
CA A:SER676 4.4 28.6 1.0
C A:LYS673 4.4 35.8 1.0
N A:ASP672 4.4 38.5 1.0
CB A:ASP672 4.5 33.7 1.0
CA A:LYS670 4.6 37.3 1.0
C A:LYS670 4.6 36.4 1.0
CB A:TYR669 4.6 29.6 1.0
O A:LYS673 4.7 37.0 1.0
N A:GLN674 4.8 36.9 1.0
CB A:SER676 5.0 30.5 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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