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Sodium in PDB 7g68: Crystal Structure of Rat Autotaxin in Complex with 2-[6-Chloro-3-[4- (2-Methoxyphenyl)Piperidine-1-Carbonyl]-5-Methylindol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles C1(=Cn(C2C1CC(C(C2)Cl)C)Cc(=O)N(C)C) C(=O)N1CC[C@@H](C2C(Oc)CCCC2)CC1 with IC50=1.09041 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[6-Chloro-3-[4- (2-Methoxyphenyl)Piperidine-1-Carbonyl]-5-Methylindol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles C1(=Cn(C2C1CC(C(C2)Cl)C)Cc(=O)N(C)C) C(=O)N1CC[C@@H](C2C(Oc)CCCC2)CC1 with IC50=1.09041 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[6-Chloro-3-[4- (2-Methoxyphenyl)Piperidine-1-Carbonyl]-5-Methylindol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles C1(=Cn(C2C1CC(C(C2)Cl)C)Cc(=O)N(C)C) C(=O)N1CC[C@@H](C2C(Oc)CCCC2)CC1 with IC50=1.09041 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[6-Chloro-3-[4- (2-Methoxyphenyl)Piperidine-1-Carbonyl]-5-Methylindol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles C1(=Cn(C2C1CC(C(C2)Cl)C)Cc(=O)N(C)C) C(=O)N1CC[C@@H](C2C(Oc)CCCC2)CC1 with IC50=1.09041 Microm, PDB code: 7g68 was solved by M.Stihle, J.Benz, D.Hunziker, H.Ratni, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.04 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.43, 92.087, 120.241, 90, 90, 90
R / Rfree (%) 20.8 / 24.9

Other elements in 7g68:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[6-Chloro-3-[4- (2-Methoxyphenyl)Piperidine-1-Carbonyl]-5-Methylindol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles C1(=Cn(C2C1CC(C(C2)Cl)C)Cc(=O)N(C)C) C(=O)N1CC[C@@H](C2C(Oc)CCCC2)CC1 with IC50=1.09041 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 2-[6-Chloro-3-[4- (2-Methoxyphenyl)Piperidine-1-Carbonyl]-5-Methylindol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles C1(=Cn(C2C1CC(C(C2)Cl)C)Cc(=O)N(C)C) C(=O)N1CC[C@@H](C2C(Oc)CCCC2)CC1 with IC50=1.09041 Microm (pdb code 7g68). 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- (2-Methoxyphenyl)Piperidine-1-Carbonyl]-5-Methylindol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles C1(=Cn(C2C1CC(C(C2)Cl)C)Cc(=O)N(C)C) C(=O)N1CC[C@@H](C2C(Oc)CCCC2)CC1 with IC50=1.09041 Microm, PDB code: 7g68:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g68

Go back to Sodium Binding Sites List in 7g68
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[6-Chloro-3-[4- (2-Methoxyphenyl)Piperidine-1-Carbonyl]-5-Methylindol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles C1(=Cn(C2C1CC(C(C2)Cl)C)Cc(=O)N(C)C) C(=O)N1CC[C@@H](C2C(Oc)CCCC2)CC1 with IC50=1.09041 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- (2-Methoxyphenyl)Piperidine-1-Carbonyl]-5-Methylindol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles C1(=Cn(C2C1CC(C(C2)Cl)C)Cc(=O)N(C)C) C(=O)N1CC[C@@H](C2C(Oc)CCCC2)CC1 with IC50=1.09041 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:47.2
occ:1.00
 O A:HOH1348 2.3 47.7 1.0
OG A:SER807 2.4 37.0 1.0
O A:HOH1153 2.4 35.5 1.0
O A:SER804 2.5 38.8 1.0
O A:ASN801 2.6 28.8 1.0
O A:HOH1087 2.7 48.3 1.0
C A:ASN801 3.5 29.9 1.0
CB A:SER807 3.5 37.6 1.0
C A:SER804 3.6 40.5 1.0
CA A:ASP802 3.9 32.9 1.0
N A:ASP802 4.0 30.4 1.0
N A:SER807 4.1 38.5 1.0
O A:ASP802 4.1 35.5 1.0
C A:ASP802 4.2 33.9 1.0
CA A:CYS805 4.3 41.7 1.0
CA A:SER807 4.3 40.0 1.0
N A:CYS805 4.4 39.9 1.0
C A:CYS805 4.4 42.4 1.0
O A:CYS805 4.4 37.5 1.0
CB A:ASN801 4.4 29.8 1.0
O A:HOH1097 4.4 46.3 1.0
N A:SER804 4.4 32.9 1.0
CA A:ASN801 4.5 30.4 1.0
CA A:SER804 4.5 33.8 1.0
OD1 A:ASP802 4.8 35.3 1.0
O A:HOH1106 4.8 46.6 1.0
CB A:SER804 4.9 36.4 1.0
O A:HOH1284 4.9 46.9 1.0
N A:ASN806 5.0 42.2 1.0
N A:GLU803 5.0 32.4 1.0

Sodium binding site 2 out of 2 in 7g68

Go back to Sodium Binding Sites List in 7g68
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[6-Chloro-3-[4- (2-Methoxyphenyl)Piperidine-1-Carbonyl]-5-Methylindol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles C1(=Cn(C2C1CC(C(C2)Cl)C)Cc(=O)N(C)C) C(=O)N1CC[C@@H](C2C(Oc)CCCC2)CC1 with IC50=1.09041 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- (2-Methoxyphenyl)Piperidine-1-Carbonyl]-5-Methylindol-1-Yl]-N,N- Dimethylacetamide, I.E. Smiles C1(=Cn(C2C1CC(C(C2)Cl)C)Cc(=O)N(C)C) C(=O)N1CC[C@@H](C2C(Oc)CCCC2)CC1 with IC50=1.09041 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:29.6
occ:1.00
 O A:HOH1302 2.0 45.8 1.0
O A:HOH1338 2.1 46.1 1.0
O A:ASP672 2.3 34.2 1.0
O A:MET675 2.3 37.9 1.0
O A:HOH1318 2.4 46.0 1.0
O A:TYR669 2.4 39.5 1.0
C A:MET675 3.4 35.4 1.0
C A:ASP672 3.5 38.4 1.0
C A:TYR669 3.5 40.6 1.0
N A:MET675 4.2 39.5 1.0
N A:SER676 4.2 31.8 1.0
CA A:SER676 4.3 32.5 1.0
CA A:LYS673 4.3 43.5 1.0
CA A:TYR669 4.3 37.2 1.0
N A:LYS673 4.4 39.4 1.0
C A:LYS673 4.4 41.2 1.0
CA A:MET675 4.4 36.4 1.0
O A:HOH1372 4.5 54.8 1.0
O A:LYS670 4.5 49.3 1.0
O A:LYS673 4.5 41.1 1.0
CA A:ASP672 4.5 39.4 1.0
N A:LYS670 4.5 41.7 1.0
CB A:TYR669 4.7 34.7 1.0
CB A:ASP672 4.7 41.8 1.0
CA A:LYS670 4.7 43.2 1.0
N A:ASP672 4.7 44.5 1.0
C A:LYS670 4.8 43.2 1.0
CB A:SER676 4.8 31.3 1.0
N A:GLN674 4.8 39.8 1.0
C A:GLN674 4.9 43.4 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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