Atomistry » Sodium » PDB 7g70-7gre » 7g78
Atomistry »
  Sodium »
    PDB 7g70-7gre »
      7g78 »

Sodium in PDB 7g78: Crystal Structure of Rat Autotaxin in Complex with 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm, PDB code: 7g78 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) 46.31 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.646, 92.618, 120.88, 90, 90, 90
R / Rfree (%) 19.1 / 23.6

Other elements in 7g78:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Chlorine (Cl) 2 atoms
Zinc (Zn) 1 atom
Potassium (K) 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-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm (pdb code 7g78). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Rat Autotaxin in Complex with 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm, PDB code: 7g78:

Sodium binding site 1 out of 1 in 7g78

Go back to Sodium Binding Sites List in 7g78
Sodium binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 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-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:43.7
occ:1.00
 O A:HOH1199 2.3 44.9 1.0
OG A:SER807 2.3 28.3 1.0
O A:HOH1480 2.4 44.6 1.0
O A:SER804 2.4 29.8 1.0
O A:HOH1150 2.5 36.4 1.0
O A:ASN801 2.6 27.9 1.0
CB A:SER807 3.5 28.1 1.0
C A:ASN801 3.5 29.4 1.0
C A:SER804 3.5 32.8 1.0
CA A:ASP802 3.9 31.6 1.0
N A:SER807 4.0 32.4 1.0
O A:HOH1028 4.1 44.5 1.0
N A:ASP802 4.1 27.7 1.0
O A:ASP802 4.2 27.2 1.0
CA A:SER807 4.3 32.8 1.0
C A:ASP802 4.3 28.8 1.0
CA A:CYS805 4.3 35.4 1.0
N A:CYS805 4.4 32.7 1.0
C A:CYS805 4.4 34.8 1.0
N A:SER804 4.5 29.4 1.0
O A:CYS805 4.5 33.8 1.0
CB A:ASN801 4.5 27.0 1.0
CA A:SER804 4.5 29.6 1.0
CA A:ASN801 4.6 27.9 1.0
O A:HOH1152 4.6 37.5 1.0
OD1 A:ASP802 4.6 37.5 1.0
O A:HOH1298 4.7 38.9 1.0
CB A:SER804 4.9 33.2 1.0
C A:SER807 5.0 34.2 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: Mon Aug 18 10:06:49 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy