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Sodium in PDB 7g2z: Crystal Structure of Rat Autotaxin in Complex with 3-Cyclopropyl-5-[3- Ethyl-2-Fluoro-6-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl) Methoxy]Phenoxy]Benzonitrile, I.E. Smiles N1(C(=O) Nn=C1COC1C(C(C(CC1)Cc)F)OC1CC(Cc(C1)C#N)C1CC1)C with IC50=0.132219 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Cyclopropyl-5-[3- Ethyl-2-Fluoro-6-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl) Methoxy]Phenoxy]Benzonitrile, I.E. Smiles N1(C(=O) Nn=C1COC1C(C(C(CC1)Cc)F)OC1CC(Cc(C1)C#N)C1CC1)C with IC50=0.132219 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Cyclopropyl-5-[3- Ethyl-2-Fluoro-6-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl) Methoxy]Phenoxy]Benzonitrile, I.E. Smiles N1(C(=O) Nn=C1COC1C(C(C(CC1)Cc)F)OC1CC(Cc(C1)C#N)C1CC1)C with IC50=0.132219 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Cyclopropyl-5-[3- Ethyl-2-Fluoro-6-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl) Methoxy]Phenoxy]Benzonitrile, I.E. Smiles N1(C(=O) Nn=C1COC1C(C(C(CC1)Cc)F)OC1CC(Cc(C1)C#N)C1CC1)C with IC50=0.132219 Microm, PDB code: 7g2z was solved by M.Stihle, J.Benz, D.Hunziker, R.Billedeau, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.90 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.964, 91.79, 119.828, 90, 90, 90
R / Rfree (%) 19.9 / 24.8

Other elements in 7g2z:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Cyclopropyl-5-[3- Ethyl-2-Fluoro-6-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl) Methoxy]Phenoxy]Benzonitrile, I.E. Smiles N1(C(=O) Nn=C1COC1C(C(C(CC1)Cc)F)OC1CC(Cc(C1)C#N)C1CC1)C with IC50=0.132219 Microm also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 3-Cyclopropyl-5-[3- Ethyl-2-Fluoro-6-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl) Methoxy]Phenoxy]Benzonitrile, I.E. Smiles N1(C(=O) Nn=C1COC1C(C(C(CC1)Cc)F)OC1CC(Cc(C1)C#N)C1CC1)C with IC50=0.132219 Microm (pdb code 7g2z). 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-Cyclopropyl-5-[3- Ethyl-2-Fluoro-6-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl) Methoxy]Phenoxy]Benzonitrile, I.E. Smiles N1(C(=O) Nn=C1COC1C(C(C(CC1)Cc)F)OC1CC(Cc(C1)C#N)C1CC1)C with IC50=0.132219 Microm, PDB code: 7g2z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g2z

Go back to Sodium Binding Sites List in 7g2z
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-Cyclopropyl-5-[3- Ethyl-2-Fluoro-6-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl) Methoxy]Phenoxy]Benzonitrile, I.E. Smiles N1(C(=O) Nn=C1COC1C(C(C(CC1)Cc)F)OC1CC(Cc(C1)C#N)C1CC1)C with IC50=0.132219 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-Cyclopropyl-5-[3- Ethyl-2-Fluoro-6-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl) Methoxy]Phenoxy]Benzonitrile, I.E. Smiles N1(C(=O) Nn=C1COC1C(C(C(CC1)Cc)F)OC1CC(Cc(C1)C#N)C1CC1)C with IC50=0.132219 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:33.2
occ:1.00
 OG A:SER807 2.3 21.0 1.0
O A:SER804 2.3 19.3 1.0
O A:HOH1430 2.4 32.6 1.0
O A:HOH1214 2.4 22.9 1.0
O A:HOH1335 2.5 26.7 1.0
O A:ASN801 2.6 18.4 1.0
C A:SER804 3.4 20.9 1.0
C A:ASN801 3.5 16.5 1.0
CB A:SER807 3.5 23.9 1.0
CA A:ASP802 3.9 18.9 1.0
N A:SER807 4.0 25.1 1.0
N A:ASP802 4.1 16.4 1.0
CA A:CYS805 4.1 23.0 1.0
O A:ASP802 4.2 17.7 1.0
N A:CYS805 4.2 21.0 1.0
C A:CYS805 4.2 24.4 1.0
C A:ASP802 4.2 18.3 1.0
CA A:SER807 4.3 26.6 1.0
O A:CYS805 4.3 23.3 1.0
CA A:SER804 4.3 20.0 1.0
N A:SER804 4.4 19.3 1.0
CB A:ASN801 4.4 15.2 1.0
O A:HOH1349 4.4 33.8 1.0
CA A:ASN801 4.5 15.6 1.0
O A:HOH1168 4.6 29.6 1.0
CB A:SER804 4.7 20.6 1.0
OD1 A:ASP802 4.7 22.2 1.0
N A:ASN806 4.8 24.9 1.0
O A:HOH1117 4.9 32.5 1.0
C A:SER807 4.9 28.3 1.0

Sodium binding site 2 out of 2 in 7g2z

Go back to Sodium Binding Sites List in 7g2z
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-Cyclopropyl-5-[3- Ethyl-2-Fluoro-6-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl) Methoxy]Phenoxy]Benzonitrile, I.E. Smiles N1(C(=O) Nn=C1COC1C(C(C(CC1)Cc)F)OC1CC(Cc(C1)C#N)C1CC1)C with IC50=0.132219 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-Cyclopropyl-5-[3- Ethyl-2-Fluoro-6-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl) Methoxy]Phenoxy]Benzonitrile, I.E. Smiles N1(C(=O) Nn=C1COC1C(C(C(CC1)Cc)F)OC1CC(Cc(C1)C#N)C1CC1)C with IC50=0.132219 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:29.3
occ:1.00
 O A:TYR669 2.2 25.7 1.0
O A:MET675 2.3 25.0 1.0
O A:ASP672 2.3 28.1 1.0
O A:HOH1426 2.4 27.4 1.0
O A:HOH1445 2.7 37.8 1.0
C A:MET675 3.4 23.3 1.0
C A:TYR669 3.4 24.8 1.0
C A:ASP672 3.5 27.4 1.0
CA A:TYR669 4.2 22.8 1.0
N A:MET675 4.2 26.7 1.0
N A:SER676 4.3 19.0 1.0
CA A:SER676 4.3 18.2 1.0
CA A:MET675 4.4 23.3 1.0
O A:HOH1468 4.4 28.2 1.0
O A:LYS670 4.4 31.2 1.0
N A:LYS670 4.4 25.7 1.0
N A:LYS673 4.4 26.7 1.0
CA A:LYS673 4.4 29.2 1.0
CA A:ASP672 4.5 26.8 1.0
C A:LYS673 4.5 27.1 1.0
CA A:LYS670 4.5 27.8 1.0
C A:LYS670 4.5 27.6 1.0
CB A:TYR669 4.6 22.1 1.0
N A:ASP672 4.6 28.5 1.0
CB A:ASP672 4.7 24.5 1.0
O A:LYS673 4.7 28.8 1.0
N A:GLN674 5.0 26.8 1.0
CB A:SER676 5.0 17.4 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 23:11:47 2025

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