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Sodium in PDB 7g6x: Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(4-Sulfamoylbutanoyl)Piperazin- 1-Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles Ns(=O)(=O)Cccc(=O) N1CCN(C2CCC3C(C2)C(=O)N(C=N3)Cc(=O)NCC2CCC(C(C2)Cl)Cl)CC1 with IC50=0.00464057 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(4-Sulfamoylbutanoyl)Piperazin- 1-Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles Ns(=O)(=O)Cccc(=O) N1CCN(C2CCC3C(C2)C(=O)N(C=N3)Cc(=O)NCC2CCC(C(C2)Cl)Cl)CC1 with IC50=0.00464057 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(4-Sulfamoylbutanoyl)Piperazin- 1-Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles Ns(=O)(=O)Cccc(=O) N1CCN(C2CCC3C(C2)C(=O)N(C=N3)Cc(=O)NCC2CCC(C(C2)Cl)Cl)CC1 with IC50=0.00464057 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(4-Sulfamoylbutanoyl)Piperazin- 1-Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles Ns(=O)(=O)Cccc(=O) N1CCN(C2CCC3C(C2)C(=O)N(C=N3)Cc(=O)NCC2CCC(C(C2)Cl)Cl)CC1 with IC50=0.00464057 Microm, PDB code: 7g6x was solved by M.Stihle, J.Benz, D.Hunziker, E.Martin-Rainer, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.97 / 1.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.076, 91.944, 119.761, 90, 90, 90
R / Rfree (%) 18.2 / 21.3

Other elements in 7g6x:

The structure of Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(4-Sulfamoylbutanoyl)Piperazin- 1-Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles Ns(=O)(=O)Cccc(=O) N1CCN(C2CCC3C(C2)C(=O)N(C=N3)Cc(=O)NCC2CCC(C(C2)Cl)Cl)CC1 with IC50=0.00464057 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 N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(4-Sulfamoylbutanoyl)Piperazin- 1-Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles Ns(=O)(=O)Cccc(=O) N1CCN(C2CCC3C(C2)C(=O)N(C=N3)Cc(=O)NCC2CCC(C(C2)Cl)Cl)CC1 with IC50=0.00464057 Microm (pdb code 7g6x). 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 N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(4-Sulfamoylbutanoyl)Piperazin- 1-Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles Ns(=O)(=O)Cccc(=O) N1CCN(C2CCC3C(C2)C(=O)N(C=N3)Cc(=O)NCC2CCC(C(C2)Cl)Cl)CC1 with IC50=0.00464057 Microm, PDB code: 7g6x:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g6x

Go back to Sodium Binding Sites List in 7g6x
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(4-Sulfamoylbutanoyl)Piperazin- 1-Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles Ns(=O)(=O)Cccc(=O) N1CCN(C2CCC3C(C2)C(=O)N(C=N3)Cc(=O)NCC2CCC(C(C2)Cl)Cl)CC1 with IC50=0.00464057 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 N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(4-Sulfamoylbutanoyl)Piperazin- 1-Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles Ns(=O)(=O)Cccc(=O) N1CCN(C2CCC3C(C2)C(=O)N(C=N3)Cc(=O)NCC2CCC(C(C2)Cl)Cl)CC1 with IC50=0.00464057 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:28.7
occ:1.00
 OG A:SER807 2.2 24.3 1.0
O A:HOH1541 2.4 32.5 1.0
O A:SER804 2.4 24.9 1.0
O A:HOH1446 2.4 32.6 1.0
O A:ASN801 2.5 21.5 1.0
O A:HOH1362 2.5 31.8 1.0
C A:ASN801 3.3 20.0 1.0
CB A:SER807 3.4 23.2 1.0
C A:SER804 3.5 23.4 1.0
CA A:ASP802 3.9 23.9 1.0
N A:ASP802 4.0 22.2 1.0
N A:SER807 4.0 26.7 1.0
O A:HOH1644 4.1 49.6 1.0
C A:ASP802 4.2 22.9 1.0
CA A:CYS805 4.2 24.8 1.0
O A:HOH1161 4.2 31.9 1.0
CA A:SER807 4.3 24.1 1.0
N A:CYS805 4.3 22.9 1.0
O A:ASP802 4.3 23.4 1.0
CB A:ASN801 4.3 21.3 1.0
N A:SER804 4.3 19.6 1.0
C A:CYS805 4.4 27.1 1.0
CA A:ASN801 4.4 21.0 1.0
CA A:SER804 4.4 20.7 1.0
O A:CYS805 4.5 27.2 1.0
O A:HOH1252 4.6 32.1 1.0
OD1 A:ASP802 4.7 32.6 1.0
CB A:SER804 4.7 23.3 1.0
N A:ASN806 4.9 25.1 1.0
O A:HOH1305 4.9 37.7 1.0
N A:GLU803 5.0 21.6 1.0

Sodium binding site 2 out of 2 in 7g6x

Go back to Sodium Binding Sites List in 7g6x
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(4-Sulfamoylbutanoyl)Piperazin- 1-Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles Ns(=O)(=O)Cccc(=O) N1CCN(C2CCC3C(C2)C(=O)N(C=N3)Cc(=O)NCC2CCC(C(C2)Cl)Cl)CC1 with IC50=0.00464057 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 N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(4-Sulfamoylbutanoyl)Piperazin- 1-Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles Ns(=O)(=O)Cccc(=O) N1CCN(C2CCC3C(C2)C(=O)N(C=N3)Cc(=O)NCC2CCC(C(C2)Cl)Cl)CC1 with IC50=0.00464057 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:29.9
occ:1.00
 O A:MET675 2.3 28.2 1.0
O A:TYR669 2.3 28.5 1.0
O A:ASP672 2.3 28.0 1.0
O A:HOH1482 2.4 36.5 1.0
O A:HOH1546 2.5 51.2 1.0
O A:HOH1594 3.1 44.0 1.0
C A:TYR669 3.4 30.5 1.0
C A:MET675 3.4 27.0 1.0
C A:ASP672 3.5 28.9 1.0
N A:MET675 4.0 26.4 1.0
CA A:TYR669 4.1 26.1 1.0
CA A:MET675 4.3 25.3 1.0
O A:LYS670 4.3 32.3 1.0
CA A:LYS673 4.3 33.2 1.0
N A:SER676 4.3 22.4 1.0
N A:LYS673 4.4 28.5 1.0
N A:ASP672 4.4 28.8 1.0
CA A:SER676 4.4 22.5 1.0
CA A:ASP672 4.4 27.2 1.0
C A:LYS673 4.4 31.7 1.0
N A:LYS670 4.5 27.6 1.0
O A:HOH1622 4.5 44.9 1.0
CB A:TYR669 4.5 25.0 1.0
CB A:ASP672 4.5 27.6 1.0
C A:LYS670 4.5 29.4 1.0
CA A:LYS670 4.6 30.4 1.0
O A:LYS673 4.6 34.5 1.0
N A:GLN674 4.9 29.0 1.0
CB A:MET675 4.9 24.3 1.0
CB A:SER676 5.0 22.6 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 23:30:33 2025

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