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Sodium in PDB 7g6j: Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyridine, I.E. Smiles C1C(NCCC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=1.98688 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyridine, I.E. Smiles C1C(NCCC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=1.98688 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyridine, I.E. Smiles C1C(NCCC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=1.98688 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyridine, I.E. Smiles C1C(NCCC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=1.98688 Microm, PDB code: 7g6j was solved by M.Stihle, J.Benz, D.Hunziker, H.Kuhne, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.69 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.845, 91.372, 119.591, 90, 90, 90
R / Rfree (%) 18.8 / 23.4

Other elements in 7g6j:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyridine, I.E. Smiles C1C(NCCC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=1.98688 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-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyridine, I.E. Smiles C1C(NCCC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=1.98688 Microm (pdb code 7g6j). 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-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyridine, I.E. Smiles C1C(NCCC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=1.98688 Microm, PDB code: 7g6j:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g6j

Go back to Sodium Binding Sites List in 7g6j
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyridine, I.E. Smiles C1C(NCCC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=1.98688 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-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyridine, I.E. Smiles C1C(NCCC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=1.98688 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:35.5
occ:1.00
 O A:HOH1293 2.2 35.0 1.0
O A:SER804 2.3 30.7 1.0
OG A:SER807 2.4 29.5 1.0
O A:HOH1443 2.4 36.3 1.0
O A:HOH1321 2.5 31.1 1.0
O A:ASN801 2.5 29.1 1.0
C A:ASN801 3.4 28.9 1.0
C A:SER804 3.4 31.5 1.0
CB A:SER807 3.4 30.8 1.0
CA A:ASP802 3.9 31.3 1.0
N A:ASP802 4.0 29.2 1.0
N A:SER807 4.1 33.4 1.0
O A:ASP802 4.2 30.8 1.0
C A:ASP802 4.2 32.5 1.0
N A:CYS805 4.2 32.1 1.0
CA A:CYS805 4.3 35.6 1.0
CA A:SER807 4.3 32.9 1.0
CB A:ASN801 4.3 26.6 1.0
O A:HOH1060 4.4 41.4 1.0
N A:SER804 4.4 28.1 1.0
CA A:SER804 4.4 28.4 1.0
C A:CYS805 4.4 35.5 1.0
CA A:ASN801 4.4 29.4 1.0
O A:CYS805 4.5 37.5 1.0
O A:HOH1200 4.6 38.0 1.0
OD1 A:ASP802 4.7 40.1 1.0
CB A:SER804 4.7 31.1 1.0
O A:HOH1274 4.9 41.4 1.0
N A:ASN806 5.0 34.5 1.0

Sodium binding site 2 out of 2 in 7g6j

Go back to Sodium Binding Sites List in 7g6j
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyridine, I.E. Smiles C1C(NCCC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=1.98688 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-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyridine, I.E. Smiles C1C(NCCC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=1.98688 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:26.1
occ:1.00
 O A:ASP672 2.2 36.3 1.0
O A:HOH1433 2.2 41.5 1.0
O A:TYR669 2.3 36.7 1.0
O A:MET675 2.3 30.2 1.0
O A:HOH1380 2.3 34.6 1.0
O A:HOH1470 2.8 46.1 1.0
C A:ASP672 3.4 37.8 1.0
C A:MET675 3.4 31.1 1.0
C A:TYR669 3.4 33.5 1.0
N A:MET675 4.1 33.0 1.0
CA A:TYR669 4.2 31.1 1.0
N A:LYS673 4.2 36.5 1.0
N A:SER676 4.3 26.7 1.0
CA A:LYS673 4.3 40.2 1.0
CA A:MET675 4.3 30.9 1.0
CA A:SER676 4.3 26.2 1.0
CA A:ASP672 4.4 35.4 1.0
C A:LYS673 4.4 37.1 1.0
O A:LYS670 4.4 38.0 1.0
N A:LYS670 4.4 34.6 1.0
O A:LYS673 4.5 41.4 1.0
CB A:ASP672 4.5 36.1 1.0
N A:ASP672 4.6 39.1 1.0
CA A:LYS670 4.6 35.9 1.0
C A:LYS670 4.6 34.5 1.0
CB A:TYR669 4.6 28.3 1.0
N A:GLN674 4.8 37.4 1.0
CB A:SER676 4.9 24.0 1.0
C A:GLN674 5.0 38.1 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 23:28:33 2025

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