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Sodium in PDB 7g3r: Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(6-Oxo-4,5-Dihydro-1H-Pyridazin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles O=C1NN=C(CC1)COC1CC(C)C(C#N)CC1C(C)(C)C with IC50=0.0299365 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(6-Oxo-4,5-Dihydro-1H-Pyridazin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles O=C1NN=C(CC1)COC1CC(C)C(C#N)CC1C(C)(C)C with IC50=0.0299365 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(6-Oxo-4,5-Dihydro-1H-Pyridazin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles O=C1NN=C(CC1)COC1CC(C)C(C#N)CC1C(C)(C)C with IC50=0.0299365 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-[(6-Oxo-4,5-Dihydro-1H-Pyridazin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles O=C1NN=C(CC1)COC1CC(C)C(C#N)CC1C(C)(C)C with IC50=0.0299365 Microm, PDB code: 7g3r was solved by M.Stihle, J.Benz, D.Hunziker, H.Ratni, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.20 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.065, 92.121, 120.555, 90, 90, 90
R / Rfree (%) 18 / 23.9

Other elements in 7g3r:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(6-Oxo-4,5-Dihydro-1H-Pyridazin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles O=C1NN=C(CC1)COC1CC(C)C(C#N)CC1C(C)(C)C with IC50=0.0299365 Microm also contains other interesting chemical elements:

Calcium (Ca) 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 5-Tert-Butyl-2- Methyl-4-[(6-Oxo-4,5-Dihydro-1H-Pyridazin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles O=C1NN=C(CC1)COC1CC(C)C(C#N)CC1C(C)(C)C with IC50=0.0299365 Microm (pdb code 7g3r). 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 5-Tert-Butyl-2- Methyl-4-[(6-Oxo-4,5-Dihydro-1H-Pyridazin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles O=C1NN=C(CC1)COC1CC(C)C(C#N)CC1C(C)(C)C with IC50=0.0299365 Microm, PDB code: 7g3r:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g3r

Go back to Sodium Binding Sites List in 7g3r
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(6-Oxo-4,5-Dihydro-1H-Pyridazin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles O=C1NN=C(CC1)COC1CC(C)C(C#N)CC1C(C)(C)C with IC50=0.0299365 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-[(6-Oxo-4,5-Dihydro-1H-Pyridazin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles O=C1NN=C(CC1)COC1CC(C)C(C#N)CC1C(C)(C)C with IC50=0.0299365 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:32.5
occ:1.00
 O A:SER804 2.2 27.4 1.0
O A:HOH1242 2.3 36.3 1.0
O A:HOH1434 2.4 41.5 1.0
OG A:SER807 2.4 25.1 1.0
O A:ASN801 2.5 23.7 1.0
C A:SER804 3.3 28.2 1.0
C A:ASN801 3.3 19.1 1.0
CB A:SER807 3.4 24.2 1.0
CA A:ASP802 3.7 24.9 1.0
N A:ASP802 3.8 19.6 1.0
N A:SER807 3.9 27.1 1.0
C A:ASP802 4.1 23.9 1.0
CA A:CYS805 4.1 26.6 1.0
N A:CYS805 4.1 24.8 1.0
O A:ASP802 4.1 25.3 1.0
CA A:SER807 4.2 27.0 1.0
C A:CYS805 4.2 28.1 1.0
N A:SER804 4.2 22.4 1.0
O A:CYS805 4.3 28.5 1.0
CA A:SER804 4.3 21.3 1.0
O A:HOH1071 4.3 30.8 1.0
CB A:ASN801 4.4 21.2 1.0
CA A:ASN801 4.5 21.3 1.0
O A:HOH1113 4.5 27.8 1.0
OD1 A:ASP802 4.5 29.6 1.0
CB A:SER804 4.7 24.0 1.0
N A:ASN806 4.8 30.9 1.0
N A:GLU803 4.9 23.3 1.0
O A:HOH1295 4.9 30.8 1.0
C A:SER807 5.0 32.9 1.0
CB A:ASP802 5.0 23.2 1.0

Sodium binding site 2 out of 2 in 7g3r

Go back to Sodium Binding Sites List in 7g3r
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(6-Oxo-4,5-Dihydro-1H-Pyridazin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles O=C1NN=C(CC1)COC1CC(C)C(C#N)CC1C(C)(C)C with IC50=0.0299365 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 5-Tert-Butyl-2- Methyl-4-[(6-Oxo-4,5-Dihydro-1H-Pyridazin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles O=C1NN=C(CC1)COC1CC(C)C(C#N)CC1C(C)(C)C with IC50=0.0299365 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:16.9
occ:1.00
 O A:HOH1223 2.1 35.5 1.0
O A:ASP672 2.1 28.2 1.0
O A:TYR669 2.2 28.0 1.0
O A:HOH1427 2.2 29.3 1.0
O A:MET675 2.3 27.7 1.0
O A:HOH1400 2.3 31.2 1.0
C A:MET675 3.4 26.3 1.0
C A:ASP672 3.4 27.7 1.0
C A:TYR669 3.4 27.1 1.0
O A:HOH1392 3.9 31.0 1.0
N A:MET675 4.1 28.2 1.0
N A:SER676 4.2 21.9 1.0
CA A:LYS673 4.2 35.0 1.0
CA A:TYR669 4.2 24.9 1.0
N A:LYS673 4.3 29.3 1.0
CA A:MET675 4.3 28.7 1.0
CA A:SER676 4.3 21.4 1.0
O A:HOH1460 4.4 47.9 1.0
C A:LYS673 4.4 33.9 1.0
O A:LYS670 4.4 30.8 1.0
CA A:ASP672 4.4 28.4 1.0
N A:LYS670 4.4 32.9 1.0
O A:LYS673 4.5 32.1 1.0
N A:ASP672 4.6 36.8 1.0
CB A:TYR669 4.6 23.2 1.0
CA A:LYS670 4.6 32.8 1.0
CB A:ASP672 4.7 29.6 1.0
C A:LYS670 4.7 25.3 1.0
N A:GLN674 4.8 33.0 1.0
CB A:SER676 4.9 21.6 1.0
C A:GLN674 5.0 35.4 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 23:15:10 2025

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