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Sodium in PDB 7g6t: Crystal Structure of Rat Autotaxin in Complex with 2,4-Dichloro-N- Phenyl-5-Piperidin-1-Ylsulfonylbenzamide, I.E. Smiles S(=O)(=O) (C1CC(C(=O)NC2CCCCC2)C(CC1CL)Cl)N1CCCCC1 with IC50=3.54684 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2,4-Dichloro-N- Phenyl-5-Piperidin-1-Ylsulfonylbenzamide, I.E. Smiles S(=O)(=O) (C1CC(C(=O)NC2CCCCC2)C(CC1CL)Cl)N1CCCCC1 with IC50=3.54684 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2,4-Dichloro-N- Phenyl-5-Piperidin-1-Ylsulfonylbenzamide, I.E. Smiles S(=O)(=O) (C1CC(C(=O)NC2CCCCC2)C(CC1CL)Cl)N1CCCCC1 with IC50=3.54684 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2,4-Dichloro-N- Phenyl-5-Piperidin-1-Ylsulfonylbenzamide, I.E. Smiles S(=O)(=O) (C1CC(C(=O)NC2CCCCC2)C(CC1CL)Cl)N1CCCCC1 with IC50=3.54684 Microm, PDB code: 7g6t was solved by M.Stihle, J.Benz, D.Hunziker, R.Canesso, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.73 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.02, 91.656, 119.628, 90, 90, 90
R / Rfree (%) 19.2 / 23.9

Other elements in 7g6t:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2,4-Dichloro-N- Phenyl-5-Piperidin-1-Ylsulfonylbenzamide, I.E. Smiles S(=O)(=O) (C1CC(C(=O)NC2CCCCC2)C(CC1CL)Cl)N1CCCCC1 with IC50=3.54684 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 3 atoms
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 2,4-Dichloro-N- Phenyl-5-Piperidin-1-Ylsulfonylbenzamide, I.E. Smiles S(=O)(=O) (C1CC(C(=O)NC2CCCCC2)C(CC1CL)Cl)N1CCCCC1 with IC50=3.54684 Microm (pdb code 7g6t). 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 2,4-Dichloro-N- Phenyl-5-Piperidin-1-Ylsulfonylbenzamide, I.E. Smiles S(=O)(=O) (C1CC(C(=O)NC2CCCCC2)C(CC1CL)Cl)N1CCCCC1 with IC50=3.54684 Microm, PDB code: 7g6t:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g6t

Go back to Sodium Binding Sites List in 7g6t
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2,4-Dichloro-N- Phenyl-5-Piperidin-1-Ylsulfonylbenzamide, I.E. Smiles S(=O)(=O) (C1CC(C(=O)NC2CCCCC2)C(CC1CL)Cl)N1CCCCC1 with IC50=3.54684 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 2,4-Dichloro-N- Phenyl-5-Piperidin-1-Ylsulfonylbenzamide, I.E. Smiles S(=O)(=O) (C1CC(C(=O)NC2CCCCC2)C(CC1CL)Cl)N1CCCCC1 with IC50=3.54684 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:40.8
occ:1.00
 OG A:SER807 2.3 33.0 1.0
O A:HOH1136 2.4 36.2 1.0
O A:HOH1220 2.4 31.8 1.0
O A:HOH1267 2.4 47.0 1.0
O A:SER804 2.5 31.4 1.0
O A:ASN801 2.7 30.3 1.0
CB A:SER807 3.4 34.9 1.0
C A:SER804 3.5 35.6 1.0
C A:ASN801 3.5 31.4 1.0
CA A:ASP802 3.9 36.0 1.0
N A:SER807 4.0 39.3 1.0
N A:ASP802 4.1 32.0 1.0
CA A:CYS805 4.2 41.0 1.0
N A:CYS805 4.2 38.0 1.0
O A:ASP802 4.3 31.4 1.0
CA A:SER807 4.3 38.7 1.0
C A:ASP802 4.3 35.1 1.0
C A:CYS805 4.4 39.3 1.0
O A:CYS805 4.4 40.2 1.0
N A:SER804 4.5 31.2 1.0
CB A:ASN801 4.5 32.1 1.0
CA A:SER804 4.5 33.6 1.0
O A:HOH1095 4.6 44.6 1.0
CA A:ASN801 4.6 33.2 1.0
OD1 A:ASP802 4.7 44.4 1.0
CB A:SER804 4.9 34.1 1.0
N A:ASN806 4.9 43.3 1.0
C A:SER807 5.0 41.7 1.0

Sodium binding site 2 out of 2 in 7g6t

Go back to Sodium Binding Sites List in 7g6t
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2,4-Dichloro-N- Phenyl-5-Piperidin-1-Ylsulfonylbenzamide, I.E. Smiles S(=O)(=O) (C1CC(C(=O)NC2CCCCC2)C(CC1CL)Cl)N1CCCCC1 with IC50=3.54684 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 2,4-Dichloro-N- Phenyl-5-Piperidin-1-Ylsulfonylbenzamide, I.E. Smiles S(=O)(=O) (C1CC(C(=O)NC2CCCCC2)C(CC1CL)Cl)N1CCCCC1 with IC50=3.54684 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:26.7
occ:1.00
 O A:ASP672 2.2 38.2 1.0
O A:HOH1260 2.2 50.0 1.0
O A:HOH1240 2.3 37.8 1.0
O A:MET675 2.3 38.8 1.0
O A:TYR669 2.3 37.5 1.0
O A:HOH1254 2.3 44.7 1.0
C A:ASP672 3.4 40.3 1.0
C A:MET675 3.4 36.3 1.0
C A:TYR669 3.5 38.2 1.0
N A:MET675 4.1 38.0 1.0
N A:LYS673 4.3 40.6 1.0
CA A:TYR669 4.3 34.0 1.0
N A:SER676 4.3 32.3 1.0
CA A:LYS673 4.3 45.0 1.0
CA A:SER676 4.3 29.9 1.0
CA A:MET675 4.3 36.8 1.0
O A:LYS670 4.3 46.5 1.0
CA A:ASP672 4.4 38.9 1.0
C A:LYS673 4.4 41.8 1.0
O A:LYS673 4.5 41.7 1.0
N A:LYS670 4.5 41.9 1.0
N A:ASP672 4.6 43.7 1.0
CB A:ASP672 4.6 40.8 1.0
CA A:LYS670 4.7 42.9 1.0
CB A:TYR669 4.7 31.3 1.0
C A:LYS670 4.7 41.7 1.0
CB A:SER676 4.8 28.2 1.0
N A:GLN674 4.9 43.6 1.0
C A:GLN674 5.0 45.4 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 23:30:33 2025

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