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Sodium in PDB 7g7g: Crystal Structure of Rat Autotaxin in Complex with 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm, PDB code: 7g7g was solved by M.Stihle, J.Benz, D.Hunziker, E.Martin-Rainer, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.61 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.756, 91.705, 119.371, 90, 90, 90
R / Rfree (%) 18.6 / 20.9

Other elements in 7g7g:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
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 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm (pdb code 7g7g). 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 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm, PDB code: 7g7g:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g7g

Go back to Sodium Binding Sites List in 7g7g
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 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 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:25.5
occ:1.00
 OG A:SER807 2.3 22.9 1.0
O A:HOH1456 2.3 27.2 1.0
O A:HOH1528 2.4 30.7 1.0
O A:SER804 2.4 22.8 1.0
O A:ASN801 2.4 19.3 1.0
O A:HOH1347 2.5 26.6 1.0
C A:ASN801 3.3 18.2 1.0
CB A:SER807 3.4 23.4 1.0
C A:SER804 3.5 22.0 1.0
CA A:ASP802 3.9 20.6 1.0
N A:ASP802 4.0 19.9 1.0
N A:SER807 4.0 24.2 1.0
C A:ASP802 4.2 21.1 1.0
CA A:CYS805 4.3 22.9 1.0
CA A:SER807 4.3 22.9 1.0
O A:ASP802 4.3 21.1 1.0
CB A:ASN801 4.3 20.4 1.0
N A:SER804 4.3 18.2 1.0
N A:CYS805 4.3 22.0 1.0
O A:HOH1085 4.3 28.9 1.0
CA A:ASN801 4.3 19.6 1.0
CA A:SER804 4.4 18.1 1.0
C A:CYS805 4.4 24.7 1.0
O A:CYS805 4.5 26.9 1.0
O A:HOH1244 4.6 31.8 1.0
OD1 A:ASP802 4.7 29.9 1.0
CB A:SER804 4.7 21.5 1.0
O A:HOH1466 4.9 31.9 1.0
N A:ASN806 4.9 23.1 1.0
N A:GLU803 5.0 20.0 1.0

Sodium binding site 2 out of 2 in 7g7g

Go back to Sodium Binding Sites List in 7g7g
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 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 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:25.5
occ:1.00
 O A:TYR669 2.2 26.4 1.0
O A:MET675 2.3 26.6 1.0
O A:ASP672 2.3 26.9 1.0
O A:HOH1499 2.4 35.7 1.0
O A:HOH1509 2.7 44.8 1.0
O A:HOH1567 3.0 38.7 1.0
C A:TYR669 3.4 25.7 1.0
C A:MET675 3.4 23.7 1.0
C A:ASP672 3.5 26.7 1.0
N A:MET675 4.0 24.6 1.0
CA A:TYR669 4.1 23.3 1.0
CA A:MET675 4.3 22.6 1.0
CA A:LYS673 4.3 29.5 1.0
N A:SER676 4.3 20.7 1.0
O A:LYS670 4.3 29.8 1.0
N A:ASP672 4.4 25.7 1.0
N A:LYS670 4.4 24.8 1.0
N A:LYS673 4.4 26.9 1.0
CA A:SER676 4.4 19.9 1.0
CA A:ASP672 4.4 25.6 1.0
C A:LYS673 4.4 27.5 1.0
CB A:TYR669 4.5 23.9 1.0
C A:LYS670 4.5 26.3 1.0
CB A:ASP672 4.5 24.0 1.0
CA A:LYS670 4.5 27.1 1.0
O A:HOH1597 4.6 44.2 1.0
O A:LYS673 4.6 31.6 1.0
CB A:MET675 4.8 20.8 1.0
N A:GLN674 4.9 26.2 1.0
CB A:SER676 5.0 22.8 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 23:32:56 2025

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