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Sodium in PDB 7g4x: Crystal Structure of Rat Autotaxin in Complex with N'-(4-Butylphenyl)- N-[2-[4-(4-Methylphenyl)Sulfonylpiperazin-1-Yl]Ethyl]Oxamide, I.E. Smiles S(=O)(=O)(N1CCN(CC1)Ccnc(=O)C(=O)NC1CCC(CC1)Cccc)C1CCC(CC1)C with IC50=0.0469096 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N'-(4-Butylphenyl)- N-[2-[4-(4-Methylphenyl)Sulfonylpiperazin-1-Yl]Ethyl]Oxamide, I.E. Smiles S(=O)(=O)(N1CCN(CC1)Ccnc(=O)C(=O)NC1CCC(CC1)Cccc)C1CCC(CC1)C with IC50=0.0469096 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N'-(4-Butylphenyl)- N-[2-[4-(4-Methylphenyl)Sulfonylpiperazin-1-Yl]Ethyl]Oxamide, I.E. Smiles S(=O)(=O)(N1CCN(CC1)Ccnc(=O)C(=O)NC1CCC(CC1)Cccc)C1CCC(CC1)C with IC50=0.0469096 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with N'-(4-Butylphenyl)- N-[2-[4-(4-Methylphenyl)Sulfonylpiperazin-1-Yl]Ethyl]Oxamide, I.E. Smiles S(=O)(=O)(N1CCN(CC1)Ccnc(=O)C(=O)NC1CCC(CC1)Cccc)C1CCC(CC1)C with IC50=0.0469096 Microm, PDB code: 7g4x 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) 45.87 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.854, 91.742, 119.833, 90, 90, 90
R / Rfree (%) 19.6 / 22.6

Other elements in 7g4x:

The structure of Crystal Structure of Rat Autotaxin in Complex with N'-(4-Butylphenyl)- N-[2-[4-(4-Methylphenyl)Sulfonylpiperazin-1-Yl]Ethyl]Oxamide, I.E. Smiles S(=O)(=O)(N1CCN(CC1)Ccnc(=O)C(=O)NC1CCC(CC1)Cccc)C1CCC(CC1)C with IC50=0.0469096 Microm also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Potassium (K) 1 atom
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with N'-(4-Butylphenyl)- N-[2-[4-(4-Methylphenyl)Sulfonylpiperazin-1-Yl]Ethyl]Oxamide, I.E. Smiles S(=O)(=O)(N1CCN(CC1)Ccnc(=O)C(=O)NC1CCC(CC1)Cccc)C1CCC(CC1)C with IC50=0.0469096 Microm (pdb code 7g4x). 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'-(4-Butylphenyl)- N-[2-[4-(4-Methylphenyl)Sulfonylpiperazin-1-Yl]Ethyl]Oxamide, I.E. Smiles S(=O)(=O)(N1CCN(CC1)Ccnc(=O)C(=O)NC1CCC(CC1)Cccc)C1CCC(CC1)C with IC50=0.0469096 Microm, PDB code: 7g4x:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g4x

Go back to Sodium Binding Sites List in 7g4x
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N'-(4-Butylphenyl)- N-[2-[4-(4-Methylphenyl)Sulfonylpiperazin-1-Yl]Ethyl]Oxamide, I.E. Smiles S(=O)(=O)(N1CCN(CC1)Ccnc(=O)C(=O)NC1CCC(CC1)Cccc)C1CCC(CC1)C with IC50=0.0469096 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'-(4-Butylphenyl)- N-[2-[4-(4-Methylphenyl)Sulfonylpiperazin-1-Yl]Ethyl]Oxamide, I.E. Smiles S(=O)(=O)(N1CCN(CC1)Ccnc(=O)C(=O)NC1CCC(CC1)Cccc)C1CCC(CC1)C with IC50=0.0469096 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:26.6
occ:1.00
 O A:HOH1439 2.3 27.0 1.0
OG A:SER807 2.4 22.5 1.0
O A:HOH1460 2.4 28.5 1.0
O A:SER804 2.4 21.0 1.0
O A:HOH1316 2.4 24.4 1.0
O A:ASN801 2.5 19.4 1.0
C A:ASN801 3.4 20.1 1.0
C A:SER804 3.5 22.0 1.0
CB A:SER807 3.5 23.8 1.0
CA A:ASP802 3.9 22.4 1.0
N A:ASP802 4.0 20.7 1.0
N A:SER807 4.1 26.0 1.0
C A:ASP802 4.2 21.9 1.0
CA A:CYS805 4.2 25.2 1.0
O A:ASP802 4.2 21.2 1.0
N A:CYS805 4.3 23.5 1.0
O A:HOH1089 4.3 30.5 1.0
CA A:SER807 4.3 25.6 1.0
C A:CYS805 4.3 25.9 1.0
N A:SER804 4.4 19.6 1.0
CB A:ASN801 4.4 18.9 1.0
CA A:SER804 4.4 20.6 1.0
O A:CYS805 4.4 25.7 1.0
CA A:ASN801 4.5 19.6 1.0
O A:HOH1108 4.7 31.1 1.0
OD1 A:ASP802 4.7 27.3 1.0
CB A:SER804 4.7 21.1 1.0
N A:ASN806 4.9 26.5 1.0
O A:HOH1228 4.9 26.7 1.0

Sodium binding site 2 out of 2 in 7g4x

Go back to Sodium Binding Sites List in 7g4x
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N'-(4-Butylphenyl)- N-[2-[4-(4-Methylphenyl)Sulfonylpiperazin-1-Yl]Ethyl]Oxamide, I.E. Smiles S(=O)(=O)(N1CCN(CC1)Ccnc(=O)C(=O)NC1CCC(CC1)Cccc)C1CCC(CC1)C with IC50=0.0469096 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'-(4-Butylphenyl)- N-[2-[4-(4-Methylphenyl)Sulfonylpiperazin-1-Yl]Ethyl]Oxamide, I.E. Smiles S(=O)(=O)(N1CCN(CC1)Ccnc(=O)C(=O)NC1CCC(CC1)Cccc)C1CCC(CC1)C with IC50=0.0469096 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:54.2
occ:1.00
 O A:ASN650 2.5 27.9 1.0
OG1 A:THR567 2.5 33.0 1.0
O A:HOH1471 2.5 36.1 1.0
O A:HOH1415 2.7 32.7 1.0
O A:THR567 2.7 31.4 1.0
C A:ASN650 3.3 28.0 1.0
C A:THR567 3.5 33.5 1.0
CB A:THR567 3.7 33.5 1.0
CB A:ASN650 3.7 32.5 1.0
N A:THR567 3.8 34.4 1.0
O A:HOH1109 3.8 34.5 1.0
CA A:THR567 3.8 33.6 1.0
N A:CYS651 4.1 25.8 1.0
CA A:ASN650 4.2 30.0 1.0
CA A:CYS651 4.2 25.1 1.0
O A:HOH1222 4.5 43.1 1.0
N A:CYS568 4.5 32.5 1.0
N A:VAL652 4.5 21.9 1.0
CG2 A:THR567 4.7 34.4 1.0
C A:CYS651 4.8 23.9 1.0
CA A:CYS568 4.9 33.6 1.0
C A:CYS566 5.0 33.6 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 23:18:33 2025

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