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Sodium in PDB 7g66: Crystal Structure of Rat Autotaxin in Complex with 2-[6-Chloro-3-[4- (3-Methylpyridin-2-Yl)Piperazine-1-Carbonyl]Indol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles N1(C(=O)C2=Cn(C3CC(CCC23)Cl)Cc(=O) N(C)C)Ccn(C2NCCCC2C)CC1 with IC50=8.37688 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[6-Chloro-3-[4- (3-Methylpyridin-2-Yl)Piperazine-1-Carbonyl]Indol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles N1(C(=O)C2=Cn(C3CC(CCC23)Cl)Cc(=O) N(C)C)Ccn(C2NCCCC2C)CC1 with IC50=8.37688 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[6-Chloro-3-[4- (3-Methylpyridin-2-Yl)Piperazine-1-Carbonyl]Indol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles N1(C(=O)C2=Cn(C3CC(CCC23)Cl)Cc(=O) N(C)C)Ccn(C2NCCCC2C)CC1 with IC50=8.37688 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[6-Chloro-3-[4- (3-Methylpyridin-2-Yl)Piperazine-1-Carbonyl]Indol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles N1(C(=O)C2=Cn(C3CC(CCC23)Cl)Cc(=O) N(C)C)Ccn(C2NCCCC2C)CC1 with IC50=8.37688 Microm, PDB code: 7g66 was solved by M.Stihle, J.Benz, D.Hunziker, M.Rogers-Evans, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.05 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.45, 92.096, 119.719, 90, 90, 90
R / Rfree (%) 19.4 / 23.1

Other elements in 7g66:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[6-Chloro-3-[4- (3-Methylpyridin-2-Yl)Piperazine-1-Carbonyl]Indol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles N1(C(=O)C2=Cn(C3CC(CCC23)Cl)Cc(=O) N(C)C)Ccn(C2NCCCC2C)CC1 with IC50=8.37688 Microm also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 2-[6-Chloro-3-[4- (3-Methylpyridin-2-Yl)Piperazine-1-Carbonyl]Indol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles N1(C(=O)C2=Cn(C3CC(CCC23)Cl)Cc(=O) N(C)C)Ccn(C2NCCCC2C)CC1 with IC50=8.37688 Microm (pdb code 7g66). 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-[6-Chloro-3-[4- (3-Methylpyridin-2-Yl)Piperazine-1-Carbonyl]Indol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles N1(C(=O)C2=Cn(C3CC(CCC23)Cl)Cc(=O) N(C)C)Ccn(C2NCCCC2C)CC1 with IC50=8.37688 Microm, PDB code: 7g66:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g66

Go back to Sodium Binding Sites List in 7g66
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[6-Chloro-3-[4- (3-Methylpyridin-2-Yl)Piperazine-1-Carbonyl]Indol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles N1(C(=O)C2=Cn(C3CC(CCC23)Cl)Cc(=O) N(C)C)Ccn(C2NCCCC2C)CC1 with IC50=8.37688 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-[6-Chloro-3-[4- (3-Methylpyridin-2-Yl)Piperazine-1-Carbonyl]Indol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles N1(C(=O)C2=Cn(C3CC(CCC23)Cl)Cc(=O) N(C)C)Ccn(C2NCCCC2C)CC1 with IC50=8.37688 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:41.9
occ:1.00
 O A:HOH1359 2.3 35.4 1.0
O A:HOH1075 2.4 32.7 1.0
OG A:SER807 2.4 29.9 1.0
O A:HOH1302 2.5 41.6 1.0
O A:SER804 2.5 25.2 1.0
O A:ASN801 2.6 23.8 1.0
C A:ASN801 3.4 23.9 1.0
C A:SER804 3.6 27.3 1.0
CB A:SER807 3.6 28.3 1.0
CA A:ASP802 3.8 27.1 1.0
N A:ASP802 3.9 24.3 1.0
O A:ASP802 4.1 28.3 1.0
C A:ASP802 4.1 25.6 1.0
N A:SER807 4.2 33.1 1.0
CA A:CYS805 4.3 30.6 1.0
N A:CYS805 4.3 29.5 1.0
O A:HOH1196 4.4 38.2 1.0
O A:CYS805 4.4 29.7 1.0
C A:CYS805 4.4 30.9 1.0
N A:SER804 4.5 23.4 1.0
CA A:SER807 4.5 30.4 1.0
CA A:SER804 4.5 24.2 1.0
CB A:ASN801 4.5 22.1 1.0
CA A:ASN801 4.5 23.0 1.0
OD1 A:ASP802 4.6 30.4 1.0
O A:HOH1223 4.8 38.0 1.0
O A:HOH1144 4.8 30.3 1.0
CB A:SER804 4.9 26.9 1.0
N A:ASN806 5.0 30.8 1.0
N A:GLU803 5.0 25.3 1.0

Sodium binding site 2 out of 2 in 7g66

Go back to Sodium Binding Sites List in 7g66
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[6-Chloro-3-[4- (3-Methylpyridin-2-Yl)Piperazine-1-Carbonyl]Indol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles N1(C(=O)C2=Cn(C3CC(CCC23)Cl)Cc(=O) N(C)C)Ccn(C2NCCCC2C)CC1 with IC50=8.37688 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-[6-Chloro-3-[4- (3-Methylpyridin-2-Yl)Piperazine-1-Carbonyl]Indol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles N1(C(=O)C2=Cn(C3CC(CCC23)Cl)Cc(=O) N(C)C)Ccn(C2NCCCC2C)CC1 with IC50=8.37688 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:34.5
occ:1.00
 O A:ASP672 2.2 30.5 1.0
O A:MET675 2.3 32.0 1.0
O A:TYR669 2.3 34.5 1.0
O A:HOH1358 2.6 51.7 1.0
O A:HOH1367 2.6 47.2 1.0
C A:MET675 3.4 28.7 1.0
C A:ASP672 3.4 32.8 1.0
C A:TYR669 3.5 36.1 1.0
N A:MET675 3.9 31.1 1.0
CA A:TYR669 4.2 32.1 1.0
CA A:MET675 4.2 28.0 1.0
CA A:LYS673 4.2 36.9 1.0
N A:LYS673 4.3 33.3 1.0
N A:SER676 4.3 25.4 1.0
C A:LYS673 4.3 34.8 1.0
CA A:ASP672 4.4 32.4 1.0
CA A:SER676 4.4 24.4 1.0
O A:LYS670 4.5 39.2 1.0
N A:LYS670 4.5 36.1 1.0
N A:ASP672 4.6 37.7 1.0
O A:LYS673 4.6 35.0 1.0
CB A:ASP672 4.6 33.2 1.0
CB A:TYR669 4.6 32.8 1.0
N A:GLN674 4.7 34.3 1.0
C A:LYS670 4.7 36.0 1.0
CA A:LYS670 4.7 37.6 1.0
CB A:MET675 4.8 27.9 1.0
C A:GLN674 4.9 35.3 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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