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Sodium in PDB 7g3e: Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm, PDB code: 7g3e was solved by M.Stihle, J.Benz, D.Hunziker, E.Pinard, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.82 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.939, 91.59, 120.062, 90, 90, 90
R / Rfree (%) 17.4 / 20.7

Other elements in 7g3e:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms
Potassium (K) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm (pdb code 7g3e). 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 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm, PDB code: 7g3e:

Sodium binding site 1 out of 1 in 7g3e

Go back to Sodium Binding Sites List in 7g3e
Sodium binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 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 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:40.1
occ:1.00
 OG A:SER807 2.3 31.9 1.0
O A:HOH1356 2.4 42.1 1.0
O A:SER804 2.4 28.6 1.0
O A:HOH1264 2.5 39.8 1.0
O A:HOH1163 2.5 38.4 1.0
O A:ASN801 2.5 28.3 1.0
C A:SER804 3.4 30.5 1.0
C A:ASN801 3.4 26.1 1.0
CB A:SER807 3.5 31.1 1.0
CA A:ASP802 3.9 33.1 1.0
N A:SER807 4.0 34.7 1.0
N A:ASP802 4.0 29.2 1.0
O A:ASP802 4.1 31.6 1.0
CA A:CYS805 4.2 34.6 1.0
N A:CYS805 4.2 31.6 1.0
C A:ASP802 4.2 31.6 1.0
O A:HOH1102 4.3 41.9 1.0
CA A:SER807 4.3 36.1 1.0
C A:CYS805 4.3 34.7 1.0
N A:SER804 4.4 27.4 1.0
O A:CYS805 4.4 37.6 1.0
CA A:SER804 4.4 27.9 1.0
CB A:ASN801 4.4 28.6 1.0
O A:HOH1188 4.5 40.9 1.0
CA A:ASN801 4.5 29.1 1.0
CB A:SER804 4.7 32.0 1.0
OD1 A:ASP802 4.8 42.0 1.0
O A:HOH1213 4.9 39.8 1.0
N A:ASN806 4.9 34.4 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 23:12:39 2025

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