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Sodium in PDB 7g59: Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm, PDB code: 7g59 was solved by M.Stihle, J.Benz, D.Hunziker, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.96 / 2.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.521, 91.926, 120.213, 90, 90, 90
R / Rfree (%) 19.2 / 24.1

Other elements in 7g59:

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm also contains other interesting chemical elements:

Fluorine (F) 16 atoms
Calcium (Ca) 2 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm (pdb code 7g59). 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-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm, PDB code: 7g59:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g59

Go back to Sodium Binding Sites List in 7g59
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 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-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:45.5
occ:1.00
 O A:HOH1258 2.2 38.1 1.0
OG A:SER807 2.2 36.6 1.0
O A:HOH1315 2.4 39.5 1.0
O A:SER804 2.5 35.0 1.0
O A:HOH1116 2.5 38.6 1.0
O A:ASN801 2.6 32.6 1.0
CB A:SER807 3.4 34.9 1.0
C A:ASN801 3.5 31.2 1.0
C A:SER804 3.6 34.9 1.0
CA A:ASP802 3.9 34.9 1.0
N A:ASP802 4.0 34.4 1.0
N A:SER807 4.1 38.0 1.0
C A:ASP802 4.3 35.1 1.0
CA A:CYS805 4.3 42.1 1.0
CA A:SER807 4.3 36.5 1.0
O A:ASP802 4.3 37.1 1.0
N A:CYS805 4.3 38.3 1.0
C A:CYS805 4.4 44.4 1.0
N A:SER804 4.5 33.1 1.0
CB A:ASN801 4.5 33.2 1.0
CA A:SER804 4.5 33.4 1.0
O A:CYS805 4.5 47.8 1.0
CA A:ASN801 4.6 32.8 1.0
OD1 A:ASP802 4.6 44.2 1.0
O A:HOH1063 4.6 41.1 1.0
O A:HOH1227 4.9 44.9 1.0
CB A:SER804 5.0 35.5 1.0
N A:ASN806 5.0 46.3 1.0

Sodium binding site 2 out of 2 in 7g59

Go back to Sodium Binding Sites List in 7g59
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 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-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:28.3
occ:1.00
 O A:ACT912 2.0 45.7 1.0
O A:ASP672 2.1 41.4 1.0
O A:MET675 2.3 37.2 1.0
O A:HOH1290 2.3 39.6 1.0
O A:TYR669 2.4 40.8 1.0
O A:HOH1287 2.4 46.6 1.0
C A:ACT912 3.3 51.7 1.0
C A:ASP672 3.3 44.2 1.0
C A:MET675 3.4 35.2 1.0
C A:TYR669 3.5 39.0 1.0
N A:MET675 4.0 40.6 1.0
OXT A:ACT912 4.1 46.8 1.0
N A:LYS673 4.2 43.1 1.0
CA A:LYS673 4.2 46.5 1.0
CA A:MET675 4.3 35.9 1.0
N A:SER676 4.3 31.4 1.0
CH3 A:ACT912 4.3 46.3 1.0
CA A:ASP672 4.3 40.4 1.0
CA A:TYR669 4.3 37.6 1.0
C A:LYS673 4.3 46.7 1.0
CA A:SER676 4.4 30.7 1.0
O A:LYS670 4.4 49.6 1.0
CB A:ASP672 4.5 40.1 1.0
O A:LYS673 4.5 43.5 1.0
N A:LYS670 4.5 44.7 1.0
N A:ASP672 4.6 46.2 1.0
C A:LYS670 4.7 44.7 1.0
CB A:TYR669 4.7 35.5 1.0
CA A:LYS670 4.7 45.3 1.0
N A:GLN674 4.8 42.9 1.0
C A:GLN674 4.9 43.7 1.0
CB A:SER676 4.9 32.1 1.0
CB A:MET675 5.0 35.2 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: Sat Feb 8 23:20:49 2025

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