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Sodium in PDB 7g33: Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm, PDB code: 7g33 was solved by M.Stihle, J.Benz, D.Hunziker, J.Plancher, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.81 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.176, 91.747, 119.809, 90, 90, 90
R / Rfree (%) 18.5 / 22.2

Other elements in 7g33:

The structure of Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 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 (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm (pdb code 7g33). 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 (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm, PDB code: 7g33:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g33

Go back to Sodium Binding Sites List in 7g33
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 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 (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:26.7
occ:1.00
 OG A:SER807 2.3 20.1 1.0
O A:SER804 2.4 17.8 1.0
O A:HOH1604 2.4 30.0 1.0
O A:HOH1380 2.4 28.5 1.0
O A:ASN801 2.5 17.4 1.0
O A:HOH1372 2.6 25.7 1.0
C A:ASN801 3.4 17.9 1.0
CB A:SER807 3.4 21.1 1.0
C A:SER804 3.4 16.7 1.0
CA A:ASP802 3.8 18.8 1.0
N A:ASP802 4.0 18.0 1.0
N A:SER807 4.0 21.1 1.0
O A:HOH1701 4.2 43.4 1.0
C A:ASP802 4.2 18.7 1.0
CA A:SER807 4.2 21.4 1.0
CA A:CYS805 4.2 19.1 1.0
N A:CYS805 4.3 18.0 1.0
O A:ASP802 4.3 17.7 1.0
O A:HOH1136 4.3 33.0 1.0
C A:CYS805 4.3 21.0 1.0
N A:SER804 4.3 15.3 1.0
CB A:ASN801 4.3 17.4 1.0
CA A:SER804 4.4 15.7 1.0
O A:CYS805 4.4 22.2 1.0
CA A:ASN801 4.4 16.5 1.0
CB A:SER804 4.7 17.3 1.0
O A:HOH1160 4.7 28.6 1.0
OD1 A:ASP802 4.7 25.7 1.0
N A:ASN806 4.8 20.1 1.0
O A:HOH1641 4.9 45.4 1.0
C A:SER807 4.9 25.1 1.0
O A:HOH1254 5.0 27.9 1.0
N A:GLU803 5.0 15.9 1.0

Sodium binding site 2 out of 2 in 7g33

Go back to Sodium Binding Sites List in 7g33
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 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 (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:23.1
occ:1.00
 O A:MET675 2.3 23.6 1.0
O A:TYR669 2.3 22.1 1.0
O A:ASP672 2.4 23.8 1.0
O A:HOH1526 2.5 31.3 1.0
O A:HOH1616 2.7 42.4 1.0
C A:TYR669 3.4 22.7 1.0
C A:MET675 3.5 22.4 1.0
C A:ASP672 3.5 24.1 1.0
N A:MET675 4.0 22.1 1.0
CA A:TYR669 4.1 20.8 1.0
O A:HOH1720 4.2 43.8 1.0
CA A:MET675 4.3 20.4 1.0
CA A:LYS673 4.4 27.3 1.0
O A:LYS670 4.4 28.9 1.0
N A:SER676 4.4 19.0 1.0
CA A:SER676 4.4 18.5 1.0
N A:LYS673 4.4 24.3 1.0
CA A:ASP672 4.4 23.5 1.0
N A:LYS670 4.4 23.3 1.0
C A:LYS673 4.5 25.9 1.0
N A:ASP672 4.5 25.3 1.0
CB A:TYR669 4.5 20.6 1.0
O A:HOH1671 4.5 37.8 1.0
CB A:ASP672 4.5 22.8 1.0
C A:LYS670 4.6 24.8 1.0
CA A:LYS670 4.6 26.7 1.0
O A:LYS673 4.7 27.1 1.0
N A:GLN674 4.8 23.6 1.0
CB A:MET675 4.9 20.9 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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