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Sodium in PDB 7g7v: Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm, PDB code: 7g7v was solved by M.Stihle, J.Benz, D.Hunziker, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.64 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.307, 92.43, 119.114, 90, 90, 90
R / Rfree (%) 18 / 21.5

Other elements in 7g7v:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm (pdb code 7g7v). 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-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm, PDB code: 7g7v:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g7v

Go back to Sodium Binding Sites List in 7g7v
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 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-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:27.9
occ:1.00
 OG A:SER807 2.3 22.6 1.0
O A:HOH1492 2.3 31.1 1.0
O A:SER804 2.4 22.6 1.0
O A:HOH1342 2.4 28.9 1.0
O A:ASN801 2.5 20.3 1.0
O A:HOH1299 2.5 30.8 1.0
C A:ASN801 3.3 20.4 1.0
CB A:SER807 3.4 22.4 1.0
C A:SER804 3.4 22.0 1.0
CA A:ASP802 3.8 25.4 1.0
N A:ASP802 3.9 23.2 1.0
N A:SER807 4.0 24.9 1.0
C A:ASP802 4.2 20.6 1.0
O A:ASP802 4.2 21.1 1.0
CA A:SER807 4.3 25.7 1.0
CA A:CYS805 4.3 25.8 1.0
CB A:ASN801 4.3 20.8 1.0
N A:CYS805 4.3 21.8 1.0
N A:SER804 4.3 18.3 1.0
C A:CYS805 4.4 27.8 1.0
CA A:SER804 4.4 19.2 1.0
CA A:ASN801 4.4 20.0 1.0
O A:HOH1184 4.4 35.6 1.0
O A:CYS805 4.4 29.4 1.0
OD1 A:ASP802 4.7 28.1 1.0
CB A:SER804 4.7 21.4 1.0
O A:HOH1280 4.7 35.1 1.0
O A:HOH1152 4.7 33.4 1.0
N A:ASN806 4.9 25.6 1.0
N A:GLU803 5.0 19.6 1.0

Sodium binding site 2 out of 2 in 7g7v

Go back to Sodium Binding Sites List in 7g7v
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 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-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:28.0
occ:1.00
 O A:ASP672 2.3 29.0 1.0
O A:TYR669 2.3 26.3 1.0
O A:MET675 2.3 25.4 1.0
O A:HOH1326 2.4 30.9 1.0
O A:HOH1529 3.0 43.9 1.0
C A:MET675 3.4 25.6 1.0
C A:TYR669 3.4 28.1 1.0
C A:ASP672 3.5 28.5 1.0
N A:MET675 4.0 27.0 1.0
CA A:TYR669 4.1 21.9 1.0
O A:LYS670 4.3 32.9 1.0
CA A:MET675 4.3 25.9 1.0
N A:SER676 4.3 21.7 1.0
N A:ASP672 4.4 26.9 1.0
CA A:LYS673 4.4 32.3 1.0
N A:LYS673 4.4 28.6 1.0
CA A:ASP672 4.4 27.6 1.0
CA A:SER676 4.4 21.7 1.0
N A:LYS670 4.5 25.9 1.0
C A:LYS673 4.5 29.9 1.0
O A:HOH1557 4.5 45.1 1.0
CB A:TYR669 4.5 25.1 1.0
C A:LYS670 4.5 29.4 1.0
CB A:ASP672 4.5 25.4 1.0
CA A:LYS670 4.6 30.7 1.0
O A:LYS673 4.7 32.8 1.0
CB A:MET675 4.9 23.6 1.0
N A:GLN674 4.9 27.2 1.0
C A:GLN674 5.0 29.3 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 23:35:26 2025

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