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Sodium in PDB 7g2k: Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm, PDB code: 7g2k 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) 45.78 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.892, 91.556, 119.073, 90, 90, 90
R / Rfree (%) 17.6 / 22.4

Other elements in 7g2k:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 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 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm (pdb code 7g2k). 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-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm, PDB code: 7g2k:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g2k

Go back to Sodium Binding Sites List in 7g2k
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 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-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:32.6
occ:1.00
 OG A:SER807 2.3 26.8 1.0
O A:HOH1053 2.4 28.6 1.0
O A:HOH1211 2.4 29.3 1.0
O A:SER804 2.4 27.8 1.0
O A:HOH1372 2.5 42.8 1.0
O A:ASN801 2.6 26.0 1.0
C A:ASN801 3.4 26.1 1.0
C A:SER804 3.5 26.4 1.0
CB A:SER807 3.6 28.2 1.0
CA A:ASP802 3.8 28.6 1.0
N A:ASP802 3.9 25.4 1.0
O A:ASP802 4.1 29.6 1.0
C A:ASP802 4.1 26.5 1.0
N A:SER807 4.2 31.5 1.0
N A:CYS805 4.2 27.3 1.0
CA A:CYS805 4.3 31.1 1.0
O A:HOH1125 4.3 41.1 1.0
N A:SER804 4.4 26.0 1.0
CA A:SER804 4.4 25.2 1.0
CB A:ASN801 4.4 26.8 1.0
C A:CYS805 4.4 31.0 1.0
CA A:SER807 4.4 30.7 1.0
CA A:ASN801 4.5 27.0 1.0
O A:CYS805 4.5 31.3 1.0
OD1 A:ASP802 4.6 35.6 1.0
O A:HOH1076 4.7 39.4 1.0
CB A:SER804 4.8 25.6 1.0
O A:HOH1299 4.8 37.7 1.0
N A:ASN806 5.0 32.4 1.0
N A:GLU803 5.0 25.4 1.0

Sodium binding site 2 out of 2 in 7g2k

Go back to Sodium Binding Sites List in 7g2k
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 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-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na910

b:34.6
occ:1.00
 O A:TYR669 2.3 33.6 1.0
O A:MET675 2.3 31.1 1.0
O A:ASP672 2.3 34.3 1.0
O A:HOH1334 2.4 40.2 1.0
O A:HOH1373 2.5 54.6 1.0
O A:HOH1387 3.1 47.6 1.0
C A:TYR669 3.4 34.7 1.0
C A:MET675 3.5 30.1 1.0
C A:ASP672 3.5 35.1 1.0
N A:MET675 4.1 30.5 1.0
CA A:TYR669 4.2 31.1 1.0
CA A:LYS673 4.3 40.1 1.0
N A:SER676 4.3 26.9 1.0
CA A:MET675 4.4 30.0 1.0
N A:LYS673 4.4 33.6 1.0
O A:LYS670 4.4 38.5 1.0
CA A:SER676 4.4 25.7 1.0
C A:LYS673 4.4 34.4 1.0
CA A:ASP672 4.4 34.0 1.0
N A:LYS670 4.5 34.5 1.0
O A:LYS673 4.5 35.1 1.0
CB A:TYR669 4.5 28.9 1.0
N A:ASP672 4.5 39.9 1.0
CA A:LYS670 4.6 38.5 1.0
C A:LYS670 4.6 36.3 1.0
CB A:ASP672 4.7 34.5 1.0
N A:GLN674 4.9 31.9 1.0
CB A:SER676 4.9 26.1 1.0
CB A:MET675 5.0 30.2 1.0
C A:GLN674 5.0 34.6 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 23:09:27 2025

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